Index: galaxy-central/tool-data/alignseq.loc
===================================================================
--- galaxy-central/tool-data/alignseq.loc (revision 3)
+++ galaxy-central/tool-data/alignseq.loc (revision 3)
@@ -0,0 +1,57 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use alignment data stored as axt files (lines starting with "align")
+#or nib files (lines starting with "seq").  You will need to index 
+#them and then create an alignseq.loc file similar to this one (store
+#it in this directory) that points to the directories in which those 
+#alignments are stored.  The "align" data referred to by the alignseq.loc 
+#file has this format (white space characters are TAB characters):
+#
+#align	<build1>	<build2>	<dir>
+#
+#So, for example, if you had hg18/bosTau2 alignment files stored in 
+#/depot/data2/galaxy/hg18/align/bosTau2, then the alignseq.loc entry 
+#would look like this:
+#
+#align	hg18	bosTau2	/depot/data2/galaxy/hg18/align/bosTau2
+#
+#and your /depot/data2/galaxy/hg18/align/bosTau2 directory would 
+#contain all of your alignment files (e.g.):
+#
+#-rw-rw-r--   1 nate   galaxy 151842783 2006-01-08 01:00 chr10.axt
+#-rw-rw-r--   1 nate   galaxy     79575 2006-01-08 01:00 chr10_random.axt
+#-rw-rw-r--   1 nate   galaxy 155015634 2006-01-08 01:01 chr11.axt
+#...etc...
+#
+#Your alignseq.loc file should include an entry per line for each alignment 
+#file you have stored.  For example:
+#
+#align anoGam1 dm1 /depot/data2/galaxy/anoGam1/align/dm1
+#align anoGam1 dm2 /depot/data2/galaxy/anoGam1/align/dm2
+#align canFam1 hg17 /depot/data2/galaxy/canFam1/align/hg17
+#...etc...
+#
+#The "seq" data referred to by the alignseq.loc file has this 
+#format (white space characters are TAB characters):
+#
+#seq	<build1>	<dir>
+#
+#So, for example, if you had anoGam1 sequence files stored in
+#/depot/data2/galaxy/anoGam1/seq, then the alignseq.loc entry
+#would look like this:
+#
+#seq anoGam1 /depot/data2/galaxy/anoGam1/seq
+#and your seq anoGam1 /depot/data2/galaxy/anoGam1/seq directory would
+#contain all of your sequence files (e.g.):
+#
+#-rw-rw-r-- 1 nate galaxy 24397551 2006-06-26 12:51 chr2L.nib
+#-rw-rw-r-- 1 nate galaxy 31362964 2006-06-26 12:51 chr2R.nib
+#-rw-rw-r-- 1 nate galaxy 20642013 2006-06-26 12:51 chr3L.nib
+#-rw-rw-r-- 1 nate galaxy 26636071 2006-06-26 12:51 chr3R.nib
+#
+#Your alignseq.loc file should include an entry per line for each sequence
+#file you have stored.  For example:
+#
+#seq anoGam1 /depot/data2/galaxy/anoGam1/seq
+#seq bosTau2 /depot/data2/galaxy/bosTau2/seq
+#seq bosTau3 /depot/data2/galaxy/bosTau3/seq
+#...etc...
Index: galaxy-central/tool-data/maf_pairwise.loc
===================================================================
--- galaxy-central/tool-data/maf_pairwise.loc (revision 3)
+++ galaxy-central/tool-data/maf_pairwise.loc (revision 3)
@@ -0,0 +1,31 @@
+#This is a sample file distributed with Galaxy that is used by some
+#alignment tools.  The maf_pairwise.loc file has this format (white 
+#space characters are TAB characters):
+#
+#<Display_name UID>	<indexed_for:build1,build2,build3>	<exists_in_maf:build1,build2,build3>	<Comma_Separated_List_of_Full_Paths_To_Files>
+#
+#Pairwise (anoGam1,dm2)	PAIRWISE_anoGam1_dm2	anoGam1,dm2	anoGam1,dm2	/depot/data2/galaxy/anoGam1/align/dm2/maf/chr2L.maf,/depot/data2/galaxy/anoGam1/align/dm2/maf/chr2R.maf,/depot/data2/galaxy/anoGam1/align/dm2/maf/chr3L.maf,/depot/data2/galaxy/anoGam1/align/dm2/maf/chr3R.maf,/depot/data2/galaxy/anoGam1/align/dm2/maf/chrM.maf,/depot/data2/galaxy/anoGam1/align/dm2/maf/chrU.maf,/depot/data2/galaxy/anoGam1/align/dm2/maf/chrX.maf
+#Pairwise (canFam1,hg17)	PAIRWISE_canFam1_hg17	canFam1,hg17	canFam1,hg17	/depot/data2/galaxy/canFam1/align/hg17/maf/chr1.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr10.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr11.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr12.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr13.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr14.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr15.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr16.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr17.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr18.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr19.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr2.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr20.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr21.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr22.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr23.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr24.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr25.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr26.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr27.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr28.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr29.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr3.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr30.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr31.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr32.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr33.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr34.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr35.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr36.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr37.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr38.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr4.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr5.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr6.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr7.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr8.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chr9.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chrM.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chrUn.maf,/depot/data2/galaxy/canFam1/align/hg17/maf/chrX.maf
+#Pairwise (canFam1,mm6)	PAIRWISE_canFam1_mm6	canFam1,mm6	canFam1,mm6	/depot/data2/galaxy/canFam1/align/mm6/maf/chr1.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr10.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr11.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr12.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr13.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr14.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr15.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr16.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr17.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr18.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr19.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr2.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr20.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr21.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr22.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr23.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr24.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr25.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr26.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr27.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr28.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr29.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr3.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr30.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr31.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr32.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr33.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr34.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr35.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr36.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr37.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr38.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr4.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr5.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr6.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr7.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr8.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chr9.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chrM.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chrUn.maf,/depot/data2/galaxy/canFam1/align/mm6/maf/chrX.maf
+#Pairwise (canFam2,canFam2)	PAIRWISE_canFam2_canFam2	canFam2,canFam2	canFam2,canFam2	/depot/data2/galaxy/canFam2/align/canFam2/maf/chr1.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr10.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr11.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr12.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr13.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr14.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr15.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr16.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr17.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr18.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr19.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr2.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr20.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr21.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr22.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr23.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr24.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr25.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr26.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr27.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr28.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr29.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr3.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr30.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr31.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr32.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr33.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr34.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr35.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr36.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr37.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr38.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr4.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr5.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr6.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr7.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr8.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chr9.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chrM.maf,/depot/data2/galaxy/canFam2/align/canFam2/maf/chrX.maf
+#Pairwise (canFam2,hg17)	PAIRWISE_canFam2_hg17	canFam2,hg17	canFam2,hg17	/depot/data2/galaxy/canFam2/align/hg17/maf/chr1.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr10.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr11.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr12.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr13.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr14.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr15.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr16.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr17.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr18.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr19.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr2.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr20.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr21.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr22.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr23.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr24.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr25.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr26.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr27.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr28.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr29.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr3.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr30.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr31.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr32.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr33.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr34.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr35.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr36.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr37.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr38.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr4.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr5.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr6.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr7.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr8.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chr9.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chrM.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chrUn.maf,/depot/data2/galaxy/canFam2/align/hg17/maf/chrX.maf
+#Pairwise (canFam2,hg18)	PAIRWISE_canFam2_hg18	canFam2,hg18	canFam2,hg18	/depot/data2/galaxy/canFam2/align/hg18/maf/chr1.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr10.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr11.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr12.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr13.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr14.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr15.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr16.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr17.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr18.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr19.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr2.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr20.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr21.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr22.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr23.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr24.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr25.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr26.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr27.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr28.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr29.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr3.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr30.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr31.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr32.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr33.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr34.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr35.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr36.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr37.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr38.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr4.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr5.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr6.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr7.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr8.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chr9.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chrM.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chrUn.maf,/depot/data2/galaxy/canFam2/align/hg18/maf/chrX.maf
+#Pairwise (canFam2,mm6)	PAIRWISE_canFam2_mm6	canFam2,mm6	canFam2,mm6	/depot/data2/galaxy/canFam2/align/mm6/maf/chr1.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr10.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr11.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr12.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr13.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr14.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr15.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr16.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr17.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr18.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr19.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr2.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr20.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr21.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr22.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr23.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr24.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr25.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr26.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr27.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr28.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr29.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr3.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr30.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr31.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr32.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr33.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr34.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr35.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr36.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr37.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr38.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr4.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr5.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr6.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr7.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr8.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chr9.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chrM.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chrUn.maf,/depot/data2/galaxy/canFam2/align/mm6/maf/chrX.maf
+#Pairwise (canFam2,mm7)	PAIRWISE_canFam2_mm7	canFam2,mm7	canFam2,mm7	/depot/data2/galaxy/canFam2/align/mm7/maf/chr1.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr10.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr11.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr12.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr13.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr14.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr15.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr16.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr17.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr18.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr19.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr2.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr20.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr21.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr22.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr23.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr24.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr25.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr26.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr27.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr28.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr29.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr3.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr30.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr31.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr32.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr33.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr34.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr35.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr36.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr37.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr38.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr4.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr5.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr6.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr7.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr8.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chr9.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chrM.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chrUn.maf,/depot/data2/galaxy/canFam2/align/mm7/maf/chrX.maf
+#Pairwise (canFam2,mm8)	PAIRWISE_canFam2_mm8	canFam2,mm8	canFam2,mm8	/depot/data2/galaxy/canFam2/align/mm8/maf/chr1.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr10.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr11.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr12.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr13.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr14.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr15.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr16.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr17.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr18.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr19.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr2.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr20.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr21.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr22.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr23.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr24.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr25.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr26.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr27.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr28.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr29.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr3.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr30.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr31.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr32.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr33.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr34.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr35.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr36.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr37.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr38.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr4.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr5.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr6.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr7.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr8.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chr9.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chrM.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chrUn.maf,/depot/data2/galaxy/canFam2/align/mm8/maf/chrX.maf
+#Pairwise (canFam2,rn3)	PAIRWISE_canFam2_rn3	canFam2,rn3	canFam2,rn3	/depot/data2/galaxy/canFam2/align/rn3/maf/chr1.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr10.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr11.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr12.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr13.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr14.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr15.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr16.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr17.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr18.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr19.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr2.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr20.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr21.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr22.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr23.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr24.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr25.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr26.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr27.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr28.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr29.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr3.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr30.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr31.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr32.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr33.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr34.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr35.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr36.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr37.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr38.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr4.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr5.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr6.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr7.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr8.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chr9.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chrM.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chrUn.maf,/depot/data2/galaxy/canFam2/align/rn3/maf/chrX.maf
+#Pairwise (canFam2,rn4)	PAIRWISE_canFam2_rn4	canFam2,rn4	canFam2,rn4	/depot/data2/galaxy/canFam2/align/rn4/maf/chr1.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr10.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr11.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr12.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr13.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr14.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr15.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr16.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr17.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr18.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr19.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr2.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr20.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr21.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr22.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr23.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr24.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr25.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr26.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr27.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr28.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr29.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr3.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr30.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr31.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr32.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr33.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr34.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr35.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr36.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr37.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr38.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr4.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr5.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr6.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr7.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr8.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chr9.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chrM.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chrUn.maf,/depot/data2/galaxy/canFam2/align/rn4/maf/chrX.maf
+#Pairwise (danRer2,fr1)	PAIRWISE_danRer2_fr1	danRer2,fr1	danRer2,fr1	/depot/data2/galaxy/danRer2/align/fr1/maf/chr1.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr10.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr11.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr12.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr13.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr14.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr15.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr16.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr17.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr18.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr19.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr2.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr20.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr21.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr22.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr23.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr24.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr25.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr3.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr4.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr5.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr6.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr7.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr8.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chr9.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chrM.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chrNA.maf,/depot/data2/galaxy/danRer2/align/fr1/maf/chrUn.maf
+#Pairwise (danRer2,hg17)	PAIRWISE_danRer2_hg17	danRer2,hg17	danRer2,hg17	/depot/data2/galaxy/danRer2/align/hg17/maf/chr1.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr10.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr11.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr12.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr13.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr14.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr15.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr16.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr17.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr18.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr19.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr2.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr20.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr21.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr22.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr23.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr24.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr25.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr3.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr4.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr5.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr6.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr7.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr8.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chr9.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chrM.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chrNA.maf,/depot/data2/galaxy/danRer2/align/hg17/maf/chrUn.maf
+#Pairwise (danRer2,mm6)	PAIRWISE_danRer2_mm6	danRer2,mm6	danRer2,mm6	/depot/data2/galaxy/danRer2/align/mm6/maf/chr1.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr10.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr11.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr12.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr13.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr14.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr15.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr16.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr17.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr18.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr19.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr2.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr20.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr21.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr22.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr23.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr24.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr25.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr3.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr4.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr5.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr6.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr7.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr8.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chr9.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chrM.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chrNA.maf,/depot/data2/galaxy/danRer2/align/mm6/maf/chrUn.maf
+#Pairwise (danRer2,tetNig1)	PAIRWISE_danRer2_tetNig1	danRer2,tetNig1	danRer2,tetNig1	/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr1.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr10.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr11.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr12.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr13.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr14.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr15.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr16.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr17.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr18.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr19.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr2.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr20.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr21.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr22.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr23.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr24.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr25.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr3.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr4.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr5.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr6.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr7.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr8.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chr9.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chrM.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chrNA.maf,/depot/data2/galaxy/danRer2/align/tetNig1/maf/chrUn.maf
+#Pairwise (danRer3,fr1)	PAIRWISE_danRer3_fr1	danRer3,fr1	danRer3,fr1	/depot/data2/galaxy/danRer3/align/fr1/maf/chr1.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr10.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr11.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr12.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr13.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr14.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr15.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr16.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr17.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr18.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr19.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr2.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr20.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr21.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr22.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr23.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr24.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr25.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr3.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr4.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr5.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr6.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr7.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr8.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chr9.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chrM.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chrNA.maf,/depot/data2/galaxy/danRer3/align/fr1/maf/chrUn.maf
+#Pairwise (danRer3,hg18)	PAIRWISE_danRer3_hg18	danRer3,hg18	danRer3,hg18	/depot/data2/galaxy/danRer3/align/hg18/maf/chr1.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr10.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr11.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr12.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr13.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr14.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr15.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr16.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr17.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr18.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr19.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr2.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr20.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr21.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr22.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr23.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr24.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr25.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr3.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr4.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr5.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr6.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr7.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr8.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chr9.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chrM.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chrNA.maf,/depot/data2/galaxy/danRer3/align/hg18/maf/chrUn.maf
+#Pairwise (danRer3,mm7)	PAIRWISE_danRer3_mm7	danRer3,mm7	danRer3,mm7	/depot/data2/galaxy/danRer3/align/mm7/maf/chr1.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr10.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr11.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr12.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr13.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr14.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr15.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr16.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr17.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr18.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr19.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr2.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr20.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr21.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr22.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr23.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr24.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr25.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr3.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr4.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr5.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr6.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr7.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr8.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chr9.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chrM.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chrNA.maf,/depot/data2/galaxy/danRer3/align/mm7/maf/chrUn.maf
+#Pairwise (danRer3,mm8)	PAIRWISE_danRer3_mm8	danRer3,mm8	danRer3,mm8	/depot/data2/galaxy/danRer3/align/mm8/maf/chr1.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr10.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr11.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr12.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr13.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr14.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr15.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr16.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr17.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr18.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr19.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr2.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr20.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr21.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr22.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr23.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr24.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr25.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr3.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr4.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr5.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr6.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr7.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr8.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chr9.maf,/depot/data2/galaxy/danRer3/align/mm8/maf/chrM.maf
+#Pairwise (danRer3,tetNig1)	PAIRWISE_danRer3_tetNig1	danRer3,tetNig1	danRer3,tetNig1	/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr1.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr10.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr11.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr12.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr13.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr14.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr15.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr16.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr17.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr18.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr19.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr2.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr20.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr21.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr22.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr23.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr24.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr25.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr3.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr4.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr5.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr6.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr7.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr8.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chr9.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chrM.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chrNA.maf,/depot/data2/galaxy/danRer3/align/tetNig1/maf/chrUn.maf
+#Pairwise (danRer4,fr1)	PAIRWISE_danRer4_fr1	danRer4,fr1	danRer4,fr1	/depot/data2/galaxy/danRer4/align/fr1/maf/chr1.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr10.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr11.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr12.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr13.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr14.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr15.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr16.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr17.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr18.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr19.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr2.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr20.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr21.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr22.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr23.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr24.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr25.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr3.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr4.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr5.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr6.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr7.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr8.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chr9.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chrM.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chrNA_random.maf,/depot/data2/galaxy/danRer4/align/fr1/maf/chrUn_random.maf
+#Pairwise (danRer4,hg18)	PAIRWISE_danRer4_hg18	danRer4,hg18	danRer4,hg18	/depot/data2/galaxy/danRer4/align/hg18/maf/chr1.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr10.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr11.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr12.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr13.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr14.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr15.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr16.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr17.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr18.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr19.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr2.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr20.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr21.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr22.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr23.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr24.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr25.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr3.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr4.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr5.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr6.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr7.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr8.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chr9.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chrM.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chrNA_random.maf,/depot/data2/galaxy/danRer4/align/hg18/maf/chrUn_random.maf
+#Pairwise (danRer4,mm8)	PAIRWISE_danRer4_mm8	danRer4,mm8	danRer4,mm8	/depot/data2/galaxy/danRer4/align/mm8/maf/chr1.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr10.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr11.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr12.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr13.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr14.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr15.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr16.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr17.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr18.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr19.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr2.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr20.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr21.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr22.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr23.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr24.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr25.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr3.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr4.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr5.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr6.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr7.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr8.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chr9.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chrM.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chrNA_random.maf,/depot/data2/galaxy/danRer4/align/mm8/maf/chrUn_random.maf
+#Pairwise (danRer4,rn4)	PAIRWISE_danRer4_rn4	danRer4,rn4	danRer4,rn4	/depot/data2/galaxy/danRer4/align/rn4/maf/chr1.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr10.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr11.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr12.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr13.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr14.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr15.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr16.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr17.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr18.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr19.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr2.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr20.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr21.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr22.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr23.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr24.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr25.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr3.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr4.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr5.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr6.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr7.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr8.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chr9.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chrM.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chrNA_random.maf,/depot/data2/galaxy/danRer4/align/rn4/maf/chrUn_random.maf
+#Pairwise (danRer4,tetNig1)	PAIRWISE_danRer4_tetNig1	danRer4,tetNig1	danRer4,tetNig1	/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr1.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr10.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr11.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr12.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr13.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr14.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr15.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr16.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr17.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr18.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr19.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr2.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr20.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr21.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr22.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr23.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr24.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr25.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr3.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr4.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr5.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr6.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr7.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr8.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chr9.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chrM.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chrNA_random.maf,/depot/data2/galaxy/danRer4/align/tetNig1/maf/chrUn_random.maf
Index: galaxy-central/tool-data/regions.loc
===================================================================
--- galaxy-central/tool-data/regions.loc (revision 3)
+++ galaxy-central/tool-data/regions.loc (revision 3)
@@ -0,0 +1,24 @@
+#This is a sample file distributed with Galaxy that is used by some
+#ENCODE tools.  The regions.loc file has this format (white space 
+#characters are TAB characters):
+#
+#<build>	<uid>	<region_description>	<file_path>
+#
+#So, for example, if you had ENCODE Regions for build hg16 stored in 
+#/depot/data2/galaxy/regions/encode_regions_coords_hg16.bed, then the
+#regions.loc entry would look like this:
+#
+#hg16    encode_hg16     ENCODE Regions  /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed
+#
+#and your /depot/data2/galaxy/regions/ directory would 
+#contain all of your regions files (e.g.):
+#
+#-rw-r--r--   1 dan  g2cache 1367 2006-03-14 13:55 encode_regions_coords_hg16.bed
+#-rw-r--r--   1 dan  g2cache 1367 2006-03-14 13:53 encode_regions_coords_hg17.bed
+#...etc...
+#
+#Your regions.loc file should include an entry per line for each region 
+#file you have stored.  For example:
+#
+#hg16	encode_hg16	ENCODE Regions	/depot/data2/galaxy/regions/encode_regions_coords_hg16.bed 
+#hg17	encode_hg17	ENCODE Regions	/depot/data2/galaxy/regions/encode_regions_coords_hg17.bed
Index: galaxy-central/tool-data/annotation_profiler_options.xml
===================================================================
--- galaxy-central/tool-data/annotation_profiler_options.xml (revision 3)
+++ galaxy-central/tool-data/annotation_profiler_options.xml (revision 3)
@@ -0,0 +1,1101 @@
+<filter type="meta_key" name="dbkey" value="hg18">
+  <options>
+    <option name="Mapping and Sequencing Tracks" value="group-map">
+        <option name="STS Markers" value="stsMap"/>
+        <option name="Fosmid End Pairs" value="fosEndPairs"/>
+        <option name="Chromosome Band" value="cytoBand"/>
+        <option name="BAC End Pairs" value="bacEndPairs"/>
+        <option name="FISH Clones" value="fishClones"/>
+        <option name="GC Percent" value="gc5Base"/>
+        <option name="Coverage" value="clonePos"/>
+        <option name="Recomb Rate" value="recombRate"/>
+        <option name="Map Contigs" value="ctgPos"/>
+        <option name="Assembly" value="gold"/>
+        <option name="Gap" value="gap"/>
+        <option name="Chromosome Band (Ideogram)" value="cytoBandIdeo"/>
+    </option>
+    <option name="Comparative Genomics" value="group-compGeno">
+        <option name="chainRn4" value="chainRn4"/>
+        <option name="chainOryLat1" value="chainOryLat1"/>
+        <option name="chainTetNig1" value="chainTetNig1"/>
+        <option name="netDanRer5" value="netDanRer5"/>
+        <option name="netPanTro2" value="netPanTro2"/>
+        <option name="chainCanFam2" value="chainCanFam2"/>
+        <option name="netPonAbe2" value="netPonAbe2"/>
+        <option name="netGasAcu1" value="netGasAcu1"/>
+        <option name="netStrPur2" value="netStrPur2"/>
+        <option name="chainDanRer5" value="chainDanRer5"/>
+        <option name="netGalGal3" value="netGalGal3"/>
+        <option name="netMonDom4" value="netMonDom4"/>
+        <option name="netOryLat1" value="netOryLat1"/>
+        <option name="netMm9" value="netMm9"/>
+        <option name="chainRheMac2" value="chainRheMac2"/>
+        <option name="netOrnAna1" value="netOrnAna1"/>
+        <option name="chainFr2" value="chainFr2"/>
+        <option name="netXenTro2" value="netXenTro2"/>
+        <option name="Cons Indels MmCf" value="consIndelsHgMmCanFam"/>
+        <option name="Tetraodon Ecores" value="ecoresTetNig1"/>
+        <option name="netTetNig1" value="netTetNig1"/>
+        <option name="chainGalGal3" value="chainGalGal3"/>
+        <option name="chainStrPur2" value="chainStrPur2"/>
+        <option name="chainOrnAna1" value="chainOrnAna1"/>
+        <option name="netFelCat3" value="netFelCat3"/>
+        <option name="chainEquCab1" value="chainEquCab1"/>
+        <option name="chainPonAbe2" value="chainPonAbe2"/>
+        <option name="chainFelCat3" value="chainFelCat3"/>
+      <option name="mostConserved28way" value="subtracks-mostConserved28way">
+        <option name="Most Conserved" value="mostConserved28way"/>
+        <option name="Vertebrate" value="phastConsElements28way"/>
+        <option name="Mammal" value="phastConsElements28wayPlacMammal"/>
+      </option>
+        <option name="chainAnoCar1" value="chainAnoCar1"/>
+        <option name="17-Way Cons" value="multiz17way"/>
+        <option name="chainXenTro2" value="chainXenTro2"/>
+        <option name="17-Way Most Cons" value="phastConsElements17way"/>
+        <option name="chainGasAcu1" value="chainGasAcu1"/>
+        <option name="Conservation" value="multiz28way"/>
+        <option name="chainCalJac1" value="chainCalJac1"/>
+        <option name="netCanFam2" value="netCanFam2"/>
+        <option name="chainMm9" value="chainMm9"/>
+        <option name="chainMonDom4" value="chainMonDom4"/>
+        <option name="netCalJac1" value="netCalJac1"/>
+        <option name="netRheMac2" value="netRheMac2"/>
+        <option name="chainPanTro2" value="chainPanTro2"/>
+        <option name="netEquCab1" value="netEquCab1"/>
+        <option name="netFr2" value="netFr2"/>
+        <option name="netAnoCar1" value="netAnoCar1"/>
+        <option name="netBosTau4" value="netBosTau4"/>
+        <option name="chainBosTau4" value="chainBosTau4"/>
+        <option name="netRn4" value="netRn4"/>
+    </option>
+    <option name="Phenotype and Disease Associations" value="group-phenDis">
+      <option name="caseControl" value="subtracks-caseControl">
+        <option name="Case Control" value="caseControl"/>
+        <option name="CCC Bipolar Dis" value="cccTrendPvalBd"/>
+        <option name="CCC Coronary Art" value="cccTrendPvalCad"/>
+        <option name="CCC Crohns Dis" value="cccTrendPvalCd"/>
+        <option name="CCC Hypertension" value="cccTrendPvalHt"/>
+        <option name="CCC Rheum Arth" value="cccTrendPvalRa"/>
+        <option name="CCC T1 Diabetes" value="cccTrendPvalT1d"/>
+        <option name="CCC T2 Diabetes" value="cccTrendPvalT2d"/>
+      </option>
+        <option name="GAD View" value="gad"/>
+        <option name="RGD Human QTL" value="rgdQtl"/>
+        <option name="RGD Rat QTL" value="rgdRatQtl"/>
+      <option name="nimhBipolar" value="subtracks-nimhBipolar">
+        <option name="NIMH Bipolar" value="nimhBipolar"/>
+        <option name="NIMH Bipolar De" value="nimhBipolarDe"/>
+        <option name="NIMH Bipolar Us" value="nimhBipolarUs"/>
+      </option>
+      <option name="jaxQtlMapped" value="subtracks-jaxQtlMapped">
+        <option name="MGI Mouse QTL" value="jaxQtlAsIs"/>
+        <option name="MGI Mouse QTL" value="jaxQtlMapped"/>
+        <option name="MGI Mouse QTL Padded" value="jaxQtlPadded"/>
+      </option>
+    </option>
+    <option name="mRNA and EST Tracks" value="group-rna">
+        <option name="CGAP SAGE" value="cgapSage"/>
+        <option name="est" value="est"/>
+        <option name="UniGene" value="uniGene_3"/>
+        <option name="Gene Bounds" value="rnaCluster"/>
+        <option name="SIB Alt-Splicing" value="sibTxGraph"/>
+        <option name="Spliced ESTs" value="intronEst"/>
+        <option name="Other mRNAs" value="xenoMrna"/>
+        <option name="H-Inv" value="HInvGeneMrna"/>
+        <option name="mrna" value="mrna"/>
+      <option name="polyA" value="subtracks-polyA">
+        <option name="Poly(A)" value="polyA"/>
+        <option name="PolyA_DB" value="polyaDb"/>
+        <option name="Poly(A) SVM" value="polyaPredict"/>
+      </option>
+        <option name="Other ESTs" value="xenoEst"/>
+    </option>
+    <option name="Genes and Gene Prediction Tracks" value="group-genes">
+        <option name="CCDS" value="ccdsGene"/>
+      <option name="augustus" value="subtracks-augustus">
+        <option name="Augustus" value="augustus"/>
+        <option name="Augustus Ab Initio" value="augustusAbinitio"/>
+        <option name="Augustus Hints" value="augustusHints"/>
+        <option name="Augustus De Novo" value="augustusXRA"/>
+      </option>
+        <option name="sno/miRNA" value="wgRna"/>
+        <option name="Geneid Genes" value="geneid"/>
+        <option name="SIB Genes" value="sibGene"/>
+        <option name="Old Known Genes" value="knownGeneOld2"/>
+        <option name="EvoFold" value="evofold"/>
+        <option name="CONTRAST" value="contrastGene"/>
+        <option name="Exoniphy" value="exoniphy"/>
+        <option name="AceView Genes" value="acembly"/>
+      <option name="nscan" value="subtracks-nscan">
+        <option name="N-SCAN" value="nscan"/>
+        <option name="N-SCAN" value="nscanGene"/>
+        <option name="N-SCAN PASA-EST" value="nscanPasaGene"/>
+      </option>
+        <option name="Ensembl Genes" value="ensGene"/>
+        <option name="SGP Genes" value="sgpGene"/>
+        <option name="RefSeq Genes" value="refGene"/>
+        <option name="Genscan Genes" value="genscan"/>
+        <option name="RNA Genes" value="rnaGene"/>
+        <option name="UCSC Genes" value="knownGene"/>
+        <option name="ACEScan" value="acescan"/>
+        <option name="Other RefSeq" value="xenoRefGene"/>
+        <option name="Alt Events" value="knownAlt"/>
+        <option name="ORFeome Clones" value="orfeomeGenes"/>
+        <option name="MGC Genes" value="mgcGenes"/>
+    </option>
+    <option name="Variation and Repeats" value="group-varRep">
+        <option name="Segmental Dups" value="genomicSuperDups"/>
+        <option name="Structural Var" value="cnp"/>
+      <option name="tajdSnp" value="subtracks-tajdSnp">
+        <option name="Tajima's D SNPs" value="tajdSnp"/>
+        <option name="SNPs AD" value="tajdSnpAd"/>
+        <option name="SNPs ED" value="tajdSnpEd"/>
+        <option name="SNPs XD" value="tajdSnpXd"/>
+      </option>
+        <option name="Self Chain" value="chainSelf"/>
+        <option name="RepeatMasker" value="rmsk"/>
+      <option name="snpArray" value="subtracks-snpArray">
+        <option name="SNP Arrays" value="snpArray"/>
+        <option name="Affy 250KNsp" value="snpArrayAffy250Nsp"/>
+        <option name="Affy 250KSty" value="snpArrayAffy250Sty"/>
+        <option name="Affy SNP 5.0" value="snpArrayAffy5"/>
+        <option name="Affy SNP 6.0" value="snpArrayAffy6"/>
+        <option name="Affy SNP 6.0 SV" value="snpArrayAffy6SV"/>
+        <option name="Illumina 300" value="snpArrayIllumina300"/>
+        <option name="Illumina 550" value="snpArrayIllumina550"/>
+        <option name="Illumina 650" value="snpArrayIllumina650"/>
+      </option>
+      <option name="hapmapLdPh" value="subtracks-hapmapLdPh">
+        <option name="HapMap LD Phased" value="hapmapLdPh"/>
+        <option name="Phased CEU" value="hapmapLdPhCeu"/>
+        <option name="Ph JPT+CHB" value="hapmapLdPhChbJpt"/>
+        <option name="Phased YRI" value="hapmapLdPhYri"/>
+      </option>
+        <option name="SNPs (126)" value="snp126"/>
+        <option name="Interrupted Rpts" value="nestedRepeats"/>
+        <option name="Exapted Repeats" value="exaptedRepeats"/>
+        <option name="SNPs (128)" value="snp128"/>
+      <option name="tajD" value="subtracks-tajD">
+        <option name="Tajima's D" value="tajD"/>
+        <option name="Tajima's D AD" value="tajdAd"/>
+        <option name="Tajima's D ED" value="tajdEd"/>
+        <option name="Tajima's D XD" value="tajdXd"/>
+      </option>
+        <option name="Microsatellite" value="microsat"/>
+        <option name="Simple Repeats" value="simpleRepeat"/>
+      <option name="hapmapSnps" value="subtracks-hapmapSnps">
+        <option name="Chimp Alleles" value="hapmapAllelesChimp"/>
+        <option name="Macaque Alleles" value="hapmapAllelesMacaque"/>
+        <option name="HapMap SNPs" value="hapmapSnps"/>
+        <option name="SNPs CEU" value="hapmapSnpsCEU"/>
+        <option name="SNPs CHB" value="hapmapSnpsCHB"/>
+        <option name="SNPs JPT" value="hapmapSnpsJPT"/>
+        <option name="SNPs YRI" value="hapmapSnpsYRI"/>
+      </option>
+    </option>
+    <option name="Expression and Regulation" value="group-regulation">
+        <option name="FirstEF" value="firstEF"/>
+        <option name="Affy GNF1H" value="affyGnf1h"/>
+        <option name="Affy All Exon" value="affyHumanExon"/>
+      <option name="wgEncodeUcsdNgTaf1Sites" value="subtracks-wgEncodeUcsdNgTaf1Sites">
+        <option name="TAF1 Known Sites" value="wgEncodeUcsdNgTaf1KnownSites"/>
+        <option name="TAF1 Novel Sites" value="wgEncodeUcsdNgTaf1NovelSites"/>
+        <option name="LI TAF1 Sites" value="wgEncodeUcsdNgTaf1Sites"/>
+      </option>
+      <option name="wgEncodeUcsdNgTaf1Valid" value="subtracks-wgEncodeUcsdNgTaf1Valid">
+        <option name="LI TAF1 Valid" value="wgEncodeUcsdNgTaf1Valid"/>
+        <option name="LI Valid H3K4m2" value="wgEncodeUcsdNgTaf1ValidH3K4me"/>
+        <option name="LI Valid H3ac" value="wgEncodeUcsdNgTaf1ValidH3ac"/>
+        <option name="LI Valid Pol2" value="wgEncodeUcsdNgTaf1ValidRnap"/>
+        <option name="LI Valid TAF1" value="wgEncodeUcsdNgTaf1ValidTaf"/>
+      </option>
+        <option name="LI TAF1 Signal" value="wgEncodeUcsdNgTaf1Signal"/>
+        <option name="Affy Txn" value="affyTxnPhase3Super"/>
+      <option name="affyTxnPhase3L" value="subtracks-affyTxnPhase3L">
+        <option name="HDF lRNA" value="affyTxnPhase3HDF"/>
+        <option name="HeLa Cyto lRNA" value="affyTxnPhase3HeLaCyto"/>
+        <option name="HeLa Nucl lRNA" value="affyTxnPhase3HeLaNuclear"/>
+        <option name="HepG2 Cyto lRNA" value="affyTxnPhase3HepG2Cyto"/>
+        <option name="HepG2 Nucl lRNA" value="affyTxnPhase3HepG2Nuclear"/>
+        <option name="Jurkat lRNA" value="affyTxnPhase3Jurkat"/>
+        <option name="Affy Tx lRNA Sig" value="affyTxnPhase3L"/>
+        <option name="NCCIT lRNA" value="affyTxnPhase3NCCIT"/>
+        <option name="PC3 lRNA" value="affyTxnPhase3PC3"/>
+        <option name="SK-N-AS lRNA" value="affyTxnPhase3SK_N_AS"/>
+        <option name="U87MG lRNA" value="affyTxnPhase3U87MG"/>
+      </option>
+        <option name="SwitchGear TSS" value="switchDbTss"/>
+        <option name="LI/UCSD TAF1" value="wgEncodeUcsdNgTaf1Super"/>
+        <option name="Affy U133Plus2" value="affyU133Plus2"/>
+        <option name="GNF Ratio" value="affyRatio"/>
+        <option name="Affy HuEx 1.0" value="affyHuEx1"/>
+      <option name="affyTxnPhase3FragsS" value="subtracks-affyTxnPhase3FragsS">
+        <option name="HeLa - sRNA" value="affyTxnPhase3FragsHeLaBottomStrand"/>
+        <option name="HeLa + sRNA" value="affyTxnPhase3FragsHeLaTopStrand"/>
+        <option name="HepG2 - sRNA" value="affyTxnPhase3FragsHepG2BottomStrand"/>
+        <option name="HepG2 + sRNA" value="affyTxnPhase3FragsHepG2TopStrand"/>
+        <option name="Affy Tx sRNA Reg" value="affyTxnPhase3FragsS"/>
+      </option>
+        <option name="7X Reg Potential" value="regPotential7X"/>
+      <option name="uppsalaChipSites" value="subtracks-uppsalaChipSites">
+        <option name="UU H3ac Sites" value="uppsalaChipH3acSites"/>
+        <option name="UU ChIP Sites" value="uppsalaChipSites"/>
+        <option name="UU Usf1 Sites" value="uppsalaChipUsf1Sites"/>
+        <option name="UU Usf2 Sites" value="uppsalaChipUsf2Sites"/>
+      </option>
+        <option name="CpG Islands" value="cpgIslandExt"/>
+        <option name="GIS PET" value="wgEncodeGisSuper"/>
+        <option name="GNF Atlas 2" value="gnfAtlas2"/>
+        <option name="Vista Enhancers" value="vistaEnhancers"/>
+      <option name="affyTxnPhase3S" value="subtracks-affyTxnPhase3S">
+        <option name="HeLa - sRNA" value="affyTxnPhase3HeLaBottomStrand"/>
+        <option name="HeLa + sRNA" value="affyTxnPhase3HeLaTopStrand"/>
+        <option name="HepG2 - sRNA" value="affyTxnPhase3HepG2BottomStrand"/>
+        <option name="HepG2 + sRNA" value="affyTxnPhase3HepG2TopStrand"/>
+        <option name="Affy Tx sRNA Sig" value="affyTxnPhase3S"/>
+      </option>
+      <option name="wgEncodeGisRnaPet" value="subtracks-wgEncodeGisRnaPet">
+        <option name="GIS PET RNA" value="wgEncodeGisRnaPet"/>
+        <option name="GIS RNA HCT116" value="wgEncodeGisRnaPetHCT116"/>
+        <option name="GIS RNA hES3" value="wgEncodeGisRnaPetHes3"/>
+        <option name="GIS RNA MCF7" value="wgEncodeGisRnaPetMCF7"/>
+        <option name="GIS RNA MCF7 Est" value="wgEncodeGisRnaPetMCF7Estr"/>
+      </option>
+        <option name="TFBS Conserved" value="tfbsConsSites"/>
+      <option name="affyTxnPhase3FragsL" value="subtracks-affyTxnPhase3FragsL">
+        <option name="HDF lRNA" value="affyTxnPhase3FragsHDF"/>
+        <option name="HeLa Cyto lRNA" value="affyTxnPhase3FragsHeLaCyto"/>
+        <option name="HeLa Nucl lRNA" value="affyTxnPhase3FragsHeLaNuclear"/>
+        <option name="HepG2 Cyto lRNA" value="affyTxnPhase3FragsHepG2Cyto"/>
+        <option name="HepG2 Nucl lRNA" value="affyTxnPhase3FragsHepG2Nuclear"/>
+        <option name="Jurkat lRNA" value="affyTxnPhase3FragsJurkat"/>
+        <option name="Affy Tx lRNA Reg" value="affyTxnPhase3FragsL"/>
+        <option name="NCCIT lRNA" value="affyTxnPhase3FragsNCCIT"/>
+        <option name="PC3 lRNA" value="affyTxnPhase3FragsPC3"/>
+        <option name="SK-N-AS lRNA" value="affyTxnPhase3FragsSK_N_AS"/>
+        <option name="U87MG lRNA" value="affyTxnPhase3FragsU87MG"/>
+      </option>
+        <option name="ORegAnno" value="oreganno"/>
+        <option name="Affy U133" value="affyU133"/>
+        <option name="Eponine TSS" value="eponine"/>
+        <option name="Allen Brain" value="allenBrainAli"/>
+        <option name="TS miRNA sites" value="targetScanS"/>
+        <option name="Bertone Yale TAR" value="yaleBertoneTars"/>
+      <option name="uppsalaChipSignal" value="subtracks-uppsalaChipSignal">
+        <option name="UU H3ac Signal" value="uppsalaChipH3acSignal"/>
+        <option name="UU ChIP Signal" value="uppsalaChipSignal"/>
+        <option name="UU Usf1 Signal" value="uppsalaChipUsf1Signal"/>
+        <option name="UU Usf2 Signal" value="uppsalaChipUsf2Signal"/>
+      </option>
+        <option name="Affy U95" value="affyU95"/>
+        <option name="Uppsala ChIP" value="uppsalaChipSuper"/>
+      <option name="wgEncodeGisChipPetAll" value="subtracks-wgEncodeGisChipPetAll">
+        <option name="p53 HCT116 +5FU" value="wgEncodeGisChipPet"/>
+        <option name="GIS ChIP-PET" value="wgEncodeGisChipPetAll"/>
+        <option name="H3K27me3 hES3" value="wgEncodeGisChipPetHes3H3K27me3"/>
+        <option name="H3K4me3 hES3" value="wgEncodeGisChipPetHes3H3K4me3"/>
+        <option name="cMyc P493" value="wgEncodeGisChipPetMycP493"/>
+        <option name="STAT1 HeLa +gIF" value="wgEncodeGisChipPetStat1Gif"/>
+        <option name="STAT1 HeLa -gIF" value="wgEncodeGisChipPetStat1NoGif"/>
+      </option>
+    </option>
+    <option name="ENCODE Comparative Genomics and Variation" value="group-encodeCompAndVar">
+        <option name="NHGRI DIPs" value="encodeIndels"/>
+    </option>
+    <option name="Experimental Tracks" value="group-x">
+        <option name="Uppsala ChIP" value="encodeUppsalaChip"/>
+      <option name="cnp" value="subtracks-cnp">
+        <option name="Iafrate CNPs" value="cnpIafrate2"/>
+        <option name="Locke CNPs" value="cnpLocke"/>
+        <option name="Redon CNPs" value="cnpRedon"/>
+        <option name="Sebat CNPs" value="cnpSebat2"/>
+        <option name="Sharp CNPs" value="cnpSharp2"/>
+        <option name="Tuzun Fosmids" value="cnpTuzun"/>
+        <option name="Conrad Dels" value="delConrad2"/>
+        <option name="Hinds Dels" value="delHinds2"/>
+        <option name="McCarroll Dels" value="delMccarroll"/>
+      </option>
+      <option name="encodeUncFaire" value="subtracks-encodeUncFaire">
+        <option name="FAIRE PeakFinder" value="encodeUncFairePeaks"/>
+        <option name="FAIRE ChIPOTle" value="encodeUncFairePeaksChipotle"/>
+      </option>
+      <option name="encodeUppsalaChipBut" value="subtracks-encodeUppsalaChipBut">
+        <option name="UU H3ac 0h vs 12h" value="encodeUppsalaChipH3acBut0vs12"/>
+        <option name="UU H4ac 0h vs 12h" value="encodeUppsalaChipH4acBut0vs12"/>
+      </option>
+        <option name="UT-Austin STAGE" value="encodeUtexStage"/>
+        <option name="UW DNase-array" value="encodeRegulomeDnaseArray"/>
+      <option name="encodeSangerChipHits" value="subtracks-encodeSangerChipHits">
+        <option name="SI H3K4m1 GM6990" value="encodeSangerChipCenterH3K4me1GM06990"/>
+        <option name="SI H3K4me1 HeLa" value="encodeSangerChipCenterH3K4me1HeLa"/>
+        <option name="SI H3K4m2 GM6990" value="encodeSangerChipCenterH3K4me2GM06990"/>
+        <option name="SI H3K4me2 HeLa" value="encodeSangerChipCenterH3K4me2HeLa"/>
+        <option name="SI H3K4me2 K562" value="encodeSangerChipCenterH3K4me2K562"/>
+        <option name="SI H3K4m3 GM6990" value="encodeSangerChipCenterH3K4me3GM06990"/>
+        <option name="SI H3K4me3 HeLa" value="encodeSangerChipCenterH3K4me3HeLa"/>
+        <option name="SI H3K4me3 K562" value="encodeSangerChipCenterH3K4me3K562"/>
+        <option name="SI H3ac GM06990" value="encodeSangerChipCenterH3acGM06990"/>
+        <option name="SI H3ac HeLa" value="encodeSangerChipCenterH3acHeLa"/>
+        <option name="SI H3ac K562" value="encodeSangerChipCenterH3acK562"/>
+        <option name="SI H4ac GM06990" value="encodeSangerChipCenterH4acGM06990"/>
+        <option name="SI H4ac HeLa" value="encodeSangerChipCenterH4acHeLa"/>
+        <option name="SI H4ac K562" value="encodeSangerChipCenterH4acK562"/>
+      </option>
+        <option name="Gencode Genes Mar07" value="encodeGencodeGeneMar07"/>
+      <option name="encodeNhgriDukeDnaseHs off" value="subtracks-encodeNhgriDukeDnaseHs off">
+        <option name="DNase CD4 MS" value="encodeNhgriDnaseHsMpssCd4"/>
+        <option name="DNase CD4-act MS" value="encodeNhgriDnaseHsMpssCd4Act"/>
+      </option>
+      <option name="encodeNhgriDukeDnaseHs" value="subtracks-encodeNhgriDukeDnaseHs">
+        <option name="DNase CD4 Pval" value="encodeNhgriDnaseHsChipPvalCd4"/>
+        <option name="DNase GM069 Pval" value="encodeNhgriDnaseHsChipPvalGm06990"/>
+        <option name="DNase H9 Pval" value="encodeNhgriDnaseHsChipPvalH9"/>
+        <option name="DNase HeLa Pval" value="encodeNhgriDnaseHsChipPvalHela"/>
+        <option name="DNase HepG2 Pval" value="encodeNhgriDnaseHsChipPvalHepG2"/>
+        <option name="DNase IMR90 Pval" value="encodeNhgriDnaseHsChipPvalImr90"/>
+        <option name="DNase K562 Pval" value="encodeNhgriDnaseHsChipPvalK562"/>
+      </option>
+    </option>
+    <option name="ENCODE Transcript Levels" value="group-encodeTxLevels">
+      <option name="encodeYaleAffyRNATars" value="subtracks-encodeYaleAffyRNATars">
+        <option name="Yale TAR NB4 RA" value="encodeYaleAffyNB4RARNATars"/>
+        <option name="Yale TAR NB4 TPA" value="encodeYaleAffyNB4TPARNATars"/>
+        <option name="Yale TAR NB4 Un" value="encodeYaleAffyNB4UntrRNATars"/>
+        <option name="Yale TAR Neutro" value="encodeYaleAffyNeutRNATars"/>
+        <option name="Yale TAR Plcnta" value="encodeYaleAffyPlacRNATars"/>
+        <option name="Yale TAR" value="encodeYaleAffyRNATars"/>
+      </option>
+      <option name="encodeYaleAffyRNATransMap" value="subtracks-encodeYaleAffyRNATransMap">
+        <option name="Yale RNA NB4 RA" value="encodeYaleAffyNB4RARNATransMap"/>
+        <option name="Yale RNA NB4 TPA" value="encodeYaleAffyNB4TPARNATransMap"/>
+        <option name="Yale RNA NB4 Un" value="encodeYaleAffyNB4UntrRNATransMap"/>
+        <option name="Yale RNA Neutro" value="encodeYaleAffyNeutRNATransMap"/>
+        <option name="Yale RNA Plcnta" value="encodeYaleAffyPlacRNATransMap"/>
+        <option name="Yale RNA" value="encodeYaleAffyRNATransMap"/>
+      </option>
+      <option name="encodeAffyRnaSignal" value="subtracks-encodeAffyRnaSignal">
+        <option name="Affy RNA GM06990" value="encodeAffyRnaGm06990Signal"/>
+        <option name="Affy RNA HeLa" value="encodeAffyRnaHeLaSignal"/>
+        <option name="Affy RNA RA 0h" value="encodeAffyRnaHl60SignalHr00"/>
+        <option name="Affy RNA RA 2h" value="encodeAffyRnaHl60SignalHr02"/>
+        <option name="Affy RNA RA 8h" value="encodeAffyRnaHl60SignalHr08"/>
+        <option name="Affy RNA RA 32h" value="encodeAffyRnaHl60SignalHr32"/>
+        <option name="Affy RNA Signal" value="encodeAffyRnaSignal"/>
+      </option>
+      <option name="encodeYaleMASPlacRNATransMap" value="subtracks-encodeYaleMASPlacRNATransMap">
+        <option name="Yale NB4 NgF RNA" value="encodeYaleMASNB4RNANprotTMFWDMless36mer36bp"/>
+        <option name="Yale NB4 NgR RNA" value="encodeYaleMASNB4RNANprotTMREVMless36mer36bp"/>
+        <option name="Yale Plc NgF RNA" value="encodeYaleMASPlacRNANprotTMFWDMless36mer36bp"/>
+        <option name="Yale Plc NgR RNA" value="encodeYaleMASPlacRNANprotTMREVMless36mer36bp"/>
+        <option name="Yale MAS RNA" value="encodeYaleMASPlacRNATransMap"/>
+        <option name="Yale Plc BtF RNA" value="encodeYaleMASPlacRNATransMapFwdMless36mer36bp"/>
+        <option name="Yale Plc BtR RNA" value="encodeYaleMASPlacRNATransMapRevMless36mer36bp"/>
+      </option>
+      <option name="encodeBuFirstExon" value="subtracks-encodeBuFirstExon">
+        <option name="BU First Exon" value="encodeBuFirstExon"/>
+        <option name="BU Cere. Cortex" value="encodeBuFirstExonCerebrum"/>
+        <option name="BU Colon" value="encodeBuFirstExonColon"/>
+        <option name="BU Heart" value="encodeBuFirstExonHeart"/>
+        <option name="BU Kidney" value="encodeBuFirstExonKidney"/>
+        <option name="BU Liver" value="encodeBuFirstExonLiver"/>
+        <option name="BU Lung" value="encodeBuFirstExonLung"/>
+        <option name="BU Skel. Muscle" value="encodeBuFirstExonSkMuscle"/>
+        <option name="BU Spleen" value="encodeBuFirstExonSpleen"/>
+        <option name="BU Stomach" value="encodeBuFirstExonStomach"/>
+        <option name="BU Testis" value="encodeBuFirstExonTestis"/>
+      </option>
+      <option name="encodeAffyEcSites" value="subtracks-encodeAffyEcSites">
+        <option name="EC1 Sites BrainC" value="encodeAffyEc1BrainCerebellumSites"/>
+        <option name="EC1 Sites BrainF" value="encodeAffyEc1BrainFrontalLobeSites"/>
+        <option name="EC1 Sites Hippoc" value="encodeAffyEc1BrainHippocampusSites"/>
+        <option name="EC1 Sites BrainH" value="encodeAffyEc1BrainHypothalamusSites"/>
+        <option name="EC1 Sites FetalK" value="encodeAffyEc1FetalKidneySites"/>
+        <option name="EC1 Sites Spleen" value="encodeAffyEc1FetalSpleenSites"/>
+        <option name="EC1 Sites FetalT" value="encodeAffyEc1FetalTestisSites"/>
+        <option name="EC1 Sites GM0699" value="encodeAffyEc1GM06990Sites"/>
+        <option name="EC1 Sites HeLa" value="encodeAffyEc1HeLaC1S3Sites"/>
+        <option name="EC1 Sites HepG2" value="encodeAffyEc1HepG2Sites"/>
+        <option name="EC1 Sites K562" value="encodeAffyEc1K562Sites"/>
+        <option name="EC1 Sites Ovary" value="encodeAffyEc1OvarySites"/>
+        <option name="EC1 Sites Placen" value="encodeAffyEc1PlacentaSites"/>
+        <option name="EC1 Sites Prost" value="encodeAffyEc1ProstateSites"/>
+        <option name="EC1 Sites TertBJ" value="encodeAffyEc1TertBJSites"/>
+        <option name="EC1 Sites Testis" value="encodeAffyEc1TestisSites"/>
+        <option name="EC51 Sites BrainC" value="encodeAffyEc51BrainCerebellumSites"/>
+        <option name="EC51 Site BrainF" value="encodeAffyEc51BrainFrontalLobeSites"/>
+        <option name="EC51 Site Hippoc" value="encodeAffyEc51BrainHippocampusSites"/>
+        <option name="EC51 Sites BrainH" value="encodeAffyEc51BrainHypothalamusSites"/>
+        <option name="EC51 Site FetalK" value="encodeAffyEc51FetalKidneySites"/>
+        <option name="EC51 Site Spleen" value="encodeAffyEc51FetalSpleenSites"/>
+        <option name="EC51 Site FetalT" value="encodeAffyEc51FetalTestisSites"/>
+        <option name="EC51 Site GM0699" value="encodeAffyEc51GM06990Sites"/>
+        <option name="EC51 Site HeLa" value="encodeAffyEc51HeLaC1S3Sites"/>
+        <option name="EC51 Site HepG2" value="encodeAffyEc51HepG2Sites"/>
+        <option name="EC51 Site K562" value="encodeAffyEc51K562Sites"/>
+        <option name="EC51 Site Ovary" value="encodeAffyEc51OvarySites"/>
+        <option name="EC51 Site Placen" value="encodeAffyEc51PlacentaSites"/>
+        <option name="EC51 Site Prost" value="encodeAffyEc51ProstateSites"/>
+        <option name="EC51 Site TertBJ" value="encodeAffyEc51TertBJSites"/>
+        <option name="EC51 Site Testis" value="encodeAffyEc51TestisSites"/>
+        <option name="Affy EC Sites" value="encodeAffyEcSites"/>
+      </option>
+      <option name="encodeStanfordPromoters" value="subtracks-encodeStanfordPromoters">
+        <option name="Stanf Promoter" value="encodeStanfordPromoters"/>
+        <option name="Stan Pro AGS" value="encodeStanfordPromotersAGS"/>
+        <option name="Stan Pro Average" value="encodeStanfordPromotersAverage"/>
+        <option name="Stan Pro Be2c" value="encodeStanfordPromotersBe2C"/>
+        <option name="Stan Pro CRL1690" value="encodeStanfordPromotersCRL1690"/>
+        <option name="Stan Pro G402" value="encodeStanfordPromotersG402"/>
+        <option name="Stan Pro HCT116" value="encodeStanfordPromotersHCT116"/>
+        <option name="Stan Pro HMCB" value="encodeStanfordPromotersHMCB"/>
+        <option name="Stan Pro HT1080" value="encodeStanfordPromotersHT1080"/>
+        <option name="Stan Pro HTB11" value="encodeStanfordPromotersHTB11"/>
+        <option name="Stan Pro Hela" value="encodeStanfordPromotersHela"/>
+        <option name="Stan Pro HepG2" value="encodeStanfordPromotersHepG2"/>
+        <option name="Stan Pro JEG3" value="encodeStanfordPromotersJEG3"/>
+        <option name="Stan Pro MG63" value="encodeStanfordPromotersMG63"/>
+        <option name="Stan Pro MRC5" value="encodeStanfordPromotersMRC5"/>
+        <option name="Stan Pro Panc1" value="encodeStanfordPromotersPanc1"/>
+        <option name="Stan Pro Snu182" value="encodeStanfordPromotersSnu182"/>
+        <option name="Stan Pro U87" value="encodeStanfordPromotersU87"/>
+      </option>
+        <option name="Affy RNA" value="encodeAffyRnaSuper"/>
+        <option name="Yale RNA" value="encodeYaleRnaSuper"/>
+      <option name="encodeAffyEcSignal" value="subtracks-encodeAffyEcSignal">
+        <option name="EC1 Sgnl BrainC" value="encodeAffyEc1BrainCerebellumSignal"/>
+        <option name="EC1 Sgnl BrainF" value="encodeAffyEc1BrainFrontalLobeSignal"/>
+        <option name="EC1 Sgnl Hippoc" value="encodeAffyEc1BrainHippocampusSignal"/>
+        <option name="EC1 Sgnl BrainH" value="encodeAffyEc1BrainHypothalamusSignal"/>
+        <option name="EC1 Sgnl FetalK" value="encodeAffyEc1FetalKidneySignal"/>
+        <option name="EC1 Sgnl Spleen" value="encodeAffyEc1FetalSpleenSignal"/>
+        <option name="EC1 Sgnl FetalT" value="encodeAffyEc1FetalTestisSignal"/>
+        <option name="EC1 Sgnl GM0699" value="encodeAffyEc1GM06990Signal"/>
+        <option name="EC1 Sgnl HeLa" value="encodeAffyEc1HeLaC1S3Signal"/>
+        <option name="EC1 Sgnl HepG2" value="encodeAffyEc1HepG2Signal"/>
+        <option name="EC1 Sgnl K562" value="encodeAffyEc1K562Signal"/>
+        <option name="EC1 Sgnl Ovary" value="encodeAffyEc1OvarySignal"/>
+        <option name="EC1 Sgnl Placen" value="encodeAffyEc1PlacentaSignal"/>
+        <option name="EC1 Sgnl Prost" value="encodeAffyEc1ProstateSignal"/>
+        <option name="EC1 Sgnl TertBJ" value="encodeAffyEc1TertBJSignal"/>
+        <option name="EC1 Sgnl Testis" value="encodeAffyEc1TestisSignal"/>
+        <option name="EC51 Sgnl BrainC" value="encodeAffyEc51BrainCerebellumSignal"/>
+        <option name="EC51 Sgnl BrainF" value="encodeAffyEc51BrainFrontalLobeSignal"/>
+        <option name="EC51 Sgnl Hippoc" value="encodeAffyEc51BrainHippocampusSignal"/>
+        <option name="EC51 Sgnl BrainH" value="encodeAffyEc51BrainHypothalamusSignal"/>
+        <option name="EC51 Sgnl FetalK" value="encodeAffyEc51FetalKidneySignal"/>
+        <option name="EC51 Sgnl Spleen" value="encodeAffyEc51FetalSpleenSignal"/>
+        <option name="EC51 Sgnl FetalT" value="encodeAffyEc51FetalTestisSignal"/>
+        <option name="EC51 Sgnl GM0699" value="encodeAffyEc51GM06990Signal"/>
+        <option name="EC51 Sgnl HeLa" value="encodeAffyEc51HeLaC1S3Signal"/>
+        <option name="EC51 Sgnl HepG2" value="encodeAffyEc51HepG2Signal"/>
+        <option name="EC51 Sgnl K562" value="encodeAffyEc51K562Signal"/>
+        <option name="EC51 Sgnl Ovary" value="encodeAffyEc51OvarySignal"/>
+        <option name="EC51 Sgnl Placen" value="encodeAffyEc51PlacentaSignal"/>
+        <option name="EC51 Sgnl Prost" value="encodeAffyEc51ProstateSignal"/>
+        <option name="EC51 Sgnl TertBJ" value="encodeAffyEc51TertBJSignal"/>
+        <option name="EC51 Sgnl Testis" value="encodeAffyEc51TestisSignal"/>
+        <option name="Affy EC Signal" value="encodeAffyEcSignal"/>
+      </option>
+        <option name="Stanf RTPCR" value="encodeStanfordRtPcr"/>
+      <option name="encodeAffyRnaTransfrags" value="subtracks-encodeAffyRnaTransfrags">
+        <option name="Affy RNA GM06990" value="encodeAffyRnaGm06990Sites"/>
+        <option name="Affy RNA HeLa" value="encodeAffyRnaHeLaSites"/>
+        <option name="Affy RNA RA 0h" value="encodeAffyRnaHl60SitesHr00"/>
+        <option name="Affy RNA RA 2h" value="encodeAffyRnaHl60SitesHr02"/>
+        <option name="Affy RNA RA 8h" value="encodeAffyRnaHl60SitesHr08"/>
+        <option name="Affy RNA RA 32h" value="encodeAffyRnaHl60SitesHr32"/>
+        <option name="Affy Transfrags" value="encodeAffyRnaTransfrags"/>
+      </option>
+      <option name="encodeYaleMASPlacRNATars" value="subtracks-encodeYaleMASPlacRNATars">
+        <option name="Yale NB4 NgF TAR" value="encodeYaleMASNB4RNANProtTarsFWDMless36mer36bp"/>
+        <option name="Yale NB4 NgR TAR" value="encodeYaleMASNB4RNANProtTarsREVMless36mer36bp"/>
+        <option name="Yale Plc NgF TAR" value="encodeYaleMASPlacRNANprotTarsFWDMless36mer36bp"/>
+        <option name="Yale Plc NgR TAR" value="encodeYaleMASPlacRNANprotTarsREVMless36mer36bp"/>
+        <option name="Yale MAS TAR" value="encodeYaleMASPlacRNATars"/>
+        <option name="Yale Plc BtF TAR" value="encodeYaleMASPlacRNATarsFwdMless36mer36bp"/>
+        <option name="Yale Plc BtR TAR" value="encodeYaleMASPlacRNATarsRevMless36mer36bp"/>
+      </option>
+        <option name="Affy EC" value="encodeAffyEcSuper"/>
+      <option name="encodeRikenCage" value="subtracks-encodeRikenCage">
+        <option name="Riken CAGE" value="encodeRikenCage"/>
+        <option name="Riken CAGE -" value="encodeRikenCageMinus"/>
+        <option name="Riken CAGE +" value="encodeRikenCagePlus"/>
+      </option>
+    </option>
+    <option name="ENCODE Chromatin Immunoprecipitation" value="group-encodeChip">
+      <option name="encodeAffyChIpHl60SignalStrict" value="subtracks-encodeAffyChIpHl60SignalStrict">
+        <option name="Affy Strict Sig" value="encodeAffyChIpHl60SignalStrict"/>
+        <option name="Affy H3K9ac2 0h" value="encodeAffyChIpHl60SignalStrictH3K9K14DHr00"/>
+        <option name="Affy H3K9ac2 2h" value="encodeAffyChIpHl60SignalStrictH3K9K14DHr02"/>
+        <option name="Affy H3K9ac2 8h" value="encodeAffyChIpHl60SignalStrictH3K9K14DHr08"/>
+        <option name="Affy H3K9ac2 32h" value="encodeAffyChIpHl60SignalStrictH3K9K14DHr32"/>
+        <option name="Affy H4Kac4 0h" value="encodeAffyChIpHl60SignalStrictHisH4Hr00"/>
+        <option name="Affy H4Kac4 2h" value="encodeAffyChIpHl60SignalStrictHisH4Hr02"/>
+        <option name="Affy H4Kac4 8h" value="encodeAffyChIpHl60SignalStrictHisH4Hr08"/>
+        <option name="Affy H4Kac4 32h" value="encodeAffyChIpHl60SignalStrictHisH4Hr32"/>
+        <option name="Affy Pol2 0h" value="encodeAffyChIpHl60SignalStrictPol2Hr00"/>
+        <option name="Affy Pol2 2h" value="encodeAffyChIpHl60SignalStrictPol2Hr02"/>
+        <option name="Affy Pol2 8h" value="encodeAffyChIpHl60SignalStrictPol2Hr08"/>
+        <option name="Affy Pol2 32h" value="encodeAffyChIpHl60SignalStrictPol2Hr32"/>
+        <option name="Affy p63 ME-180+" value="encodeAffyChIpHl60SignalStrictp63_ActD"/>
+        <option name="Affy p63 ME-180" value="encodeAffyChIpHl60SignalStrictp63_mActD"/>
+      </option>
+        <option name="Stanf ChIP" value="encodeStanfordChipSuper"/>
+      <option name="encodeYaleChIPSTAT1Pval" value="subtracks-encodeYaleChIPSTAT1Pval">
+        <option name="Yale LI PVal" value="encodeYaleChIPSTAT1HeLaBingRenPval"/>
+        <option name="Yale 36-36 PVal" value="encodeYaleChIPSTAT1HeLaMaskLess36mer36bpPval"/>
+        <option name="Yale 50-38 PVal" value="encodeYaleChIPSTAT1HeLaMaskLess50mer38bpPval"/>
+        <option name="Yale 50-50 PVal" value="encodeYaleChIPSTAT1HeLaMaskLess50mer50bpPval"/>
+        <option name="Yale STAT1 pVal" value="encodeYaleChIPSTAT1Pval"/>
+      </option>
+      <option name="encodeUtexStage" value="subtracks-encodeUtexStage">
+        <option name="UT-Austin STAGE" value="encodeUtexStage"/>
+        <option name="UT Myc HeLa Tags" value="encodeUtexStageCMycHelaTags"/>
+        <option name="UT STAT1 HeLa Tags" value="encodeUtexStageStat1HelaTags"/>
+      </option>
+        <option name="Sanger ChIP-chip" value="encodeSangerChipSuper"/>
+      <option name="encodeLIChIP" value="subtracks-encodeLIChIP">
+        <option name="LI ChIP Various" value="encodeLIChIP"/>
+        <option name="LI H3ac IMR90" value="encodeUcsdChipAch3Imr90_f"/>
+        <option name="LI H3K27me3 HeLa" value="encodeUcsdChipH3K27me3"/>
+        <option name="LI SUZ12 HeLa" value="encodeUcsdChipH3K27me3Suz12"/>
+        <option name="LI H3K4me2 IMR90" value="encodeUcsdChipMeh3k4Imr90_f"/>
+        <option name="LI Pol2 HCT116" value="encodeUcsdChipRnapHct116_f"/>
+        <option name="LI Pol2 HeLa" value="encodeUcsdChipRnapHela_f"/>
+        <option name="LI Pol2 IMR90" value="encodeUcsdChipRnapImr90_f"/>
+        <option name="LI Pol2 THP1" value="encodeUcsdChipRnapThp1_f"/>
+        <option name="LI TAF1 HCT116" value="encodeUcsdChipTaf250Hct116_f"/>
+        <option name="LI TAF1 HeLa" value="encodeUcsdChipTaf250Hela_f"/>
+        <option name="LI TAF1 IMR90" value="encodeUcsdChipTaf250Imr90_f"/>
+        <option name="LI TAF1 THP1" value="encodeUcsdChipTaf250Thp1_f"/>
+      </option>
+      <option name="encodeUtexChip" value="subtracks-encodeUtexChip">
+        <option name="UT-Austin ChIP" value="encodeUtexChip"/>
+        <option name="UT E2F4 st-Fb Pk" value="encodeUtexChip2091fibE2F4Peaks"/>
+        <option name="UT E2F4 Fb" value="encodeUtexChip2091fibE2F4Raw"/>
+        <option name="UT Myc Fb Pk" value="encodeUtexChip2091fibMycPeaks"/>
+        <option name="UT Myc Fb" value="encodeUtexChip2091fibMycRaw"/>
+        <option name="UT Myc st-Fb Pk" value="encodeUtexChip2091fibMycStimPeaks"/>
+        <option name="UT Myc st-Fb" value="encodeUtexChip2091fibMycStimRaw"/>
+        <option name="UT Myc HeLa Pk" value="encodeUtexChipHeLaMycPeaks"/>
+        <option name="UT Myc HeLa" value="encodeUtexChipHeLaMycRaw"/>
+      </option>
+      <option name="encodeYaleChipSig" value="subtracks-encodeYaleChipSig">
+        <option name="Yale ChIP Signal" value="encodeYaleChipSig"/>
+        <option name="YU BAF155 HeLa S" value="encodeYaleChipSignalBaf155"/>
+        <option name="YU BAF155 K562 S" value="encodeYaleChipSignalBaf155K562"/>
+        <option name="YU BAF170 HeLa S" value="encodeYaleChipSignalBaf170"/>
+        <option name="YU BAF170 K562 S" value="encodeYaleChipSignalBaf170K562"/>
+        <option name="YU BAF47 K562 S" value="encodeYaleChipSignalBaf47K562"/>
+        <option name="YU c-Fos HeLa S" value="encodeYaleChipSignalFos"/>
+        <option name="YU H3K27me3 HeLa S" value="encodeYaleChipSignalH3k27me3Hela"/>
+        <option name="YU H4Kac4 GM S" value="encodeYaleChipSignalH4kac4Gm06990"/>
+        <option name="YU H4Kac4 HeLa S" value="encodeYaleChipSignalH4kac4Hela"/>
+        <option name="YU c-Jun HeLa S" value="encodeYaleChipSignalJun"/>
+        <option name="YU NRSF HeLa S" value="encodeYaleChipSignalNrsfHela"/>
+        <option name="YU P65-C HeLa TNF S" value="encodeYaleChipSignalP65cHelaTnfa"/>
+        <option name="YU P65-N HeLa TNF S" value="encodeYaleChipSignalP65nHelaTnfa"/>
+        <option name="YU Pol2 GM S" value="encodeYaleChipSignalPol2Gm06990"/>
+        <option name="YU Pol2 HeLa S" value="encodeYaleChipSignalPol2Hela"/>
+        <option name="YU Pol2N GM S" value="encodeYaleChipSignalPol2nGm06990"/>
+        <option name="YU Pol2N HeLa S" value="encodeYaleChipSignalPol2nHela"/>
+        <option name="YU SMARCA4 HeLa S" value="encodeYaleChipSignalSmarca4Hela"/>
+        <option name="YU SMARCA6 HeLa S" value="encodeYaleChipSignalSmarca6Hela"/>
+        <option name="YU STAT1 HeLa IF S" value="encodeYaleChipSignalStat1HelaIfna"/>
+        <option name="YU TAF1 HeLa S" value="encodeYaleChipSignalTaf"/>
+      </option>
+        <option name="Uppsala ChIP" value="encodeUppsalaChipSuper"/>
+      <option name="encodeUppsalaChip" value="subtracks-encodeUppsalaChip">
+        <option name="Uppsala ChIP" value="encodeUppsalaChip"/>
+        <option name="UU H3ac HepG2" value="encodeUppsalaChipAch3"/>
+        <option name="UU HNF-3b HepG2" value="encodeUppsalaChipHnf3b"/>
+        <option name="UU HNF-4a HepG2" value="encodeUppsalaChipHnf4a"/>
+        <option name="UU USF-1 HepG2" value="encodeUppsalaChipUsf1"/>
+      </option>
+      <option name="encodeUcDavisChipHits" value="subtracks-encodeUcDavisChipHits">
+        <option name="UCD Ng ChIP Hits" value="encodeUcDavisChipHits"/>
+        <option name="UCD E2F1 Hits" value="encodeUcDavisChipHitsE2F1"/>
+        <option name="UCD c-Myc Hits" value="encodeUcDavisChipHitsMyc"/>
+      </option>
+      <option name="encodeUppsalaChipBut" value="subtracks-encodeUppsalaChipBut">
+        <option name="Uppsala ChIP Buty" value="encodeUppsalaChipBut"/>
+        <option name="UU H3ac HepG2 0h" value="encodeUppsalaChipH3acBut0h"/>
+        <option name="UU H3ac HepG2 12h" value="encodeUppsalaChipH3acBut12h"/>
+        <option name="UU H4ac HepG2 0h" value="encodeUppsalaChipH4acBut0h"/>
+        <option name="UU H4ac HepG2 12h" value="encodeUppsalaChipH4acBut12h"/>
+      </option>
+      <option name="encodeYaleChipSites" value="subtracks-encodeYaleChipSites">
+        <option name="Yale ChIP Sites" value="encodeYaleChipSites"/>
+        <option name="YU BAF155 HeLa" value="encodeYaleChipSitesBaf155"/>
+        <option name="YU BAF155 K562" value="encodeYaleChipSitesBaf155K562"/>
+        <option name="YU BAF170 HeLa" value="encodeYaleChipSitesBaf170"/>
+        <option name="YU BAF170 K562" value="encodeYaleChipSitesBaf170K562"/>
+        <option name="YU BAF47 K562" value="encodeYaleChipSitesBaf47K562"/>
+        <option name="YU c-Fos HeLa" value="encodeYaleChipSitesFos"/>
+        <option name="YU H3K27me3 HeLa" value="encodeYaleChipSitesH3k27me3Hela"/>
+        <option name="YU H4Kac4 GM" value="encodeYaleChipSitesH4kac4Gm06990"/>
+        <option name="YU H4Kac4 HeLa" value="encodeYaleChipSitesH4kac4Hela"/>
+        <option name="YU c-Jun HeLa" value="encodeYaleChipSitesJun"/>
+        <option name="YU NRSF HeLa" value="encodeYaleChipSitesNrsfHela"/>
+        <option name="YU P65-C HeLa TNF" value="encodeYaleChipSitesP65cHelaTnfa"/>
+        <option name="YU P65-N HeLa TNF" value="encodeYaleChipSitesP65nHelaTnfa"/>
+        <option name="YU Pol2 GM" value="encodeYaleChipSitesPol2Gm06990"/>
+        <option name="YU Pol2 HeLa" value="encodeYaleChipSitesPol2Hela"/>
+        <option name="YU Pol2N GM" value="encodeYaleChipSitesPol2nGm06990"/>
+        <option name="YU Pol2N HeLa" value="encodeYaleChipSitesPol2nHela"/>
+        <option name="YU SMARCA4 HeLa" value="encodeYaleChipSitesSmarca4Hela"/>
+        <option name="YU SMARCA6 HeLa" value="encodeYaleChipSitesSmarca6Hela"/>
+        <option name="YU STAT1 HeLa IF" value="encodeYaleChipSitesStat1HelaIfna"/>
+        <option name="YU TAF1 HeLa" value="encodeYaleChipSitesTaf"/>
+      </option>
+      <option name="encodeLIChIPgIF" value="subtracks-encodeLIChIPgIF">
+        <option name="LI gIF ChIP" value="encodeLIChIPgIF"/>
+        <option name="LI Pol2 -gIF" value="encodeUcsdChipHeLaH3H4RNAP_p0"/>
+        <option name="LI Pol2 +gIF" value="encodeUcsdChipHeLaH3H4RNAP_p30"/>
+        <option name="LI TAF1 -gIF" value="encodeUcsdChipHeLaH3H4TAF250_p0"/>
+        <option name="LI TAF1 +gIF" value="encodeUcsdChipHeLaH3H4TAF250_p30"/>
+        <option name="LI H3ac -gIF" value="encodeUcsdChipHeLaH3H4acH3_p0"/>
+        <option name="LI H3ac +gIF" value="encodeUcsdChipHeLaH3H4acH3_p30"/>
+        <option name="LI H4ac -gIF" value="encodeUcsdChipHeLaH3H4acH4_p0"/>
+        <option name="LI H4ac +gIF" value="encodeUcsdChipHeLaH3H4acH4_p30"/>
+        <option name="LI H3K4me2 -gIF" value="encodeUcsdChipHeLaH3H4dmH3K4_p0"/>
+        <option name="LI H3K4me2 +gIF" value="encodeUcsdChipHeLaH3H4dmH3K4_p30"/>
+        <option name="LI STAT1 -gIF" value="encodeUcsdChipHeLaH3H4stat1_p0"/>
+        <option name="LI STAT1 +gIF" value="encodeUcsdChipHeLaH3H4stat1_p30"/>
+        <option name="LI H3K4me3 -gIF" value="encodeUcsdChipHeLaH3H4tmH3K4_p0"/>
+        <option name="LI H3K4me3 +gIF" value="encodeUcsdChipHeLaH3H4tmH3K4_p30"/>
+      </option>
+        <option name="Yale WG ChIP-seq" value="wgEncodeYaleChipSeqSuper"/>
+      <option name="encodeStanfordChipSmoothed" value="subtracks-encodeStanfordChipSmoothed">
+        <option name="Stanf ChIP Score" value="encodeStanfordChipSmoothed"/>
+        <option name="Stan Sc HCT116 Sp1" value="encodeStanfordChipSmoothedHCT116Sp1"/>
+        <option name="Stan Sc HCT116 Sp3" value="encodeStanfordChipSmoothedHCT116Sp3"/>
+        <option name="Stan Sc Jurkat Sp1" value="encodeStanfordChipSmoothedJurkatSp1"/>
+        <option name="Stan Sc Jurkat Sp3" value="encodeStanfordChipSmoothedJurkatSp3"/>
+        <option name="Stan Sc K562 Sp1" value="encodeStanfordChipSmoothedK562Sp1"/>
+        <option name="Stan Sc K562 Sp3" value="encodeStanfordChipSmoothedK562Sp3"/>
+      </option>
+      <option name="encodeYaleChIPSTAT1Sites" value="subtracks-encodeYaleChIPSTAT1Sites">
+        <option name="Yale LI Sites" value="encodeYaleChIPSTAT1HeLaBingRenSites"/>
+        <option name="Yale 36-36 Sites" value="encodeYaleChIPSTAT1HeLaMaskLess36mer36bpSite"/>
+        <option name="Yale 50-38 Sites" value="encodeYaleChIPSTAT1HeLaMaskLess50mer38bpSite"/>
+        <option name="Yale 50-50 Sites" value="encodeYaleChIPSTAT1HeLaMaskLess50mer50bpSite"/>
+        <option name="Yale STAT1 Sites" value="encodeYaleChIPSTAT1Sites"/>
+      </option>
+        <option name="Affy ChIP" value="encodeAffyChipSuper"/>
+      <option name="encodeStanfordChip" value="subtracks-encodeStanfordChip">
+        <option name="Stanf ChIP" value="encodeStanfordChip"/>
+        <option name="Stan HCT116 Sp1" value="encodeStanfordChipHCT116Sp1"/>
+        <option name="Stan HCT116 Sp3" value="encodeStanfordChipHCT116Sp3"/>
+        <option name="Stan Jurkat Sp1" value="encodeStanfordChipJurkatSp1"/>
+        <option name="Stan Jurkat Sp3" value="encodeStanfordChipJurkatSp3"/>
+        <option name="Stan K562 Sp1" value="encodeStanfordChipK562Sp1"/>
+        <option name="Stan K562 Sp3" value="encodeStanfordChipK562Sp3"/>
+      </option>
+      <option name="encodeAffyChIpHl60SitesStrict" value="subtracks-encodeAffyChIpHl60SitesStrict">
+        <option name="Affy Strict Sites" value="encodeAffyChIpHl60SitesStrict"/>
+        <option name="Affy H3K9ac2 0h" value="encodeAffyChIpHl60SitesStrictH3K9K14DHr00"/>
+        <option name="Affy H3K9ac2 2h" value="encodeAffyChIpHl60SitesStrictH3K9K14DHr02"/>
+        <option name="Affy H3K9ac2 8h" value="encodeAffyChIpHl60SitesStrictH3K9K14DHr08"/>
+        <option name="Affy H3K9ac2 32h" value="encodeAffyChIpHl60SitesStrictH3K9K14DHr32"/>
+        <option name="Affy H4Kac4 0h" value="encodeAffyChIpHl60SitesStrictHisH4Hr00"/>
+        <option name="Affy H4Kac4 2h" value="encodeAffyChIpHl60SitesStrictHisH4Hr02"/>
+        <option name="Affy H4Kac4 8h" value="encodeAffyChIpHl60SitesStrictHisH4Hr08"/>
+        <option name="Affy H4Kac4 32h" value="encodeAffyChIpHl60SitesStrictHisH4Hr32"/>
+        <option name="Affy p63 ME-180+" value="encodeAffyChIpHl60SitesStrictP63_ActD"/>
+        <option name="Affy p63 ME-180" value="encodeAffyChIpHl60SitesStrictP63_mActD"/>
+        <option name="Affy Pol2 0h" value="encodeAffyChIpHl60SitesStrictRnapHr00"/>
+        <option name="Affy Pol2 2h" value="encodeAffyChIpHl60SitesStrictRnapHr02"/>
+        <option name="Affy Pol2 8h" value="encodeAffyChIpHl60SitesStrictRnapHr08"/>
+        <option name="Affy Pol2 32h" value="encodeAffyChIpHl60SitesStrictRnapHr32"/>
+      </option>
+      <option name="encodeAffyChIpHl60Pval" value="subtracks-encodeAffyChIpHl60Pval">
+        <option name="Affy pVal" value="encodeAffyChIpHl60Pval"/>
+        <option name="Affy Brg1 RA 0h" value="encodeAffyChIpHl60PvalBrg1Hr00"/>
+        <option name="Affy Brg1 RA 2h" value="encodeAffyChIpHl60PvalBrg1Hr02"/>
+        <option name="Affy Brg1 RA 8h" value="encodeAffyChIpHl60PvalBrg1Hr08"/>
+        <option name="Affy Brg1 RA 32h" value="encodeAffyChIpHl60PvalBrg1Hr32"/>
+        <option name="Affy CEBPe RA 0h" value="encodeAffyChIpHl60PvalCebpeHr00"/>
+        <option name="Affy CEBPe RA 2h" value="encodeAffyChIpHl60PvalCebpeHr02"/>
+        <option name="Affy CEBPe RA 8h" value="encodeAffyChIpHl60PvalCebpeHr08"/>
+        <option name="Affy CEBPe RA 32h" value="encodeAffyChIpHl60PvalCebpeHr32"/>
+        <option name="Affy CTCF RA 0h" value="encodeAffyChIpHl60PvalCtcfHr00"/>
+        <option name="Affy CTCF RA 2h" value="encodeAffyChIpHl60PvalCtcfHr02"/>
+        <option name="Affy CTCF RA 8h" value="encodeAffyChIpHl60PvalCtcfHr08"/>
+        <option name="Affy CTCF RA 32h" value="encodeAffyChIpHl60PvalCtcfHr32"/>
+        <option name="Affy H3K27me3 RA 0h" value="encodeAffyChIpHl60PvalH3K27me3Hr00"/>
+        <option name="Affy H3K27me3 RA 2h" value="encodeAffyChIpHl60PvalH3K27me3Hr02"/>
+        <option name="Affy H3K27me3 RA 8h" value="encodeAffyChIpHl60PvalH3K27me3Hr08"/>
+        <option name="Affy H3K27me3 RA 32h" value="encodeAffyChIpHl60PvalH3K27me3Hr32"/>
+        <option name="Affy H4Kac4 RA 0h" value="encodeAffyChIpHl60PvalH4Kac4Hr00"/>
+        <option name="Affy H4Kac4 RA 2h" value="encodeAffyChIpHl60PvalH4Kac4Hr02"/>
+        <option name="Affy H4Kac4 RA 8h" value="encodeAffyChIpHl60PvalH4Kac4Hr08"/>
+        <option name="Affy H4Kac4 RA 32h" value="encodeAffyChIpHl60PvalH4Kac4Hr32"/>
+        <option name="Affy P300 RA 0h" value="encodeAffyChIpHl60PvalP300Hr00"/>
+        <option name="Affy P300 RA 2h" value="encodeAffyChIpHl60PvalP300Hr02"/>
+        <option name="Affy P300 RA 8h" value="encodeAffyChIpHl60PvalP300Hr08"/>
+        <option name="Affy P300 RA 32h" value="encodeAffyChIpHl60PvalP300Hr32"/>
+        <option name="Affy PU1 RA 0h" value="encodeAffyChIpHl60PvalPu1Hr00"/>
+        <option name="Affy PU1 RA 2h" value="encodeAffyChIpHl60PvalPu1Hr02"/>
+        <option name="Affy PU1 RA 8h" value="encodeAffyChIpHl60PvalPu1Hr08"/>
+        <option name="Affy PU1 RA 32h" value="encodeAffyChIpHl60PvalPu1Hr32"/>
+        <option name="Affy RARA RA 0h" value="encodeAffyChIpHl60PvalRaraHr00"/>
+        <option name="Affy RARA RA 2h" value="encodeAffyChIpHl60PvalRaraHr02"/>
+        <option name="Affy RARA RA 8h" value="encodeAffyChIpHl60PvalRaraHr08"/>
+        <option name="Affy RARA RA 32h" value="encodeAffyChIpHl60PvalRaraHr32"/>
+        <option name="Affy Pol2 RA 0h" value="encodeAffyChIpHl60PvalRnapHr00"/>
+        <option name="Affy Pol2 RA 2h" value="encodeAffyChIpHl60PvalRnapHr02"/>
+        <option name="Affy Pol2 RA 8h" value="encodeAffyChIpHl60PvalRnapHr08"/>
+        <option name="Affy Pol2 RA 32h" value="encodeAffyChIpHl60PvalRnapHr32"/>
+        <option name="Affy SIRT1 RA 0h" value="encodeAffyChIpHl60PvalSirt1Hr00"/>
+        <option name="Affy SIRT1 RA 2h" value="encodeAffyChIpHl60PvalSirt1Hr02"/>
+        <option name="Affy SIRT1 RA 8h" value="encodeAffyChIpHl60PvalSirt1Hr08"/>
+        <option name="Affy SIRT1 RA 32h" value="encodeAffyChIpHl60PvalSirt1Hr32"/>
+        <option name="Affy TFIIB RA 32h" value="encodeAffyChIpHl60PvalTfiibHr32"/>
+      </option>
+      <option name="encodeYaleChipRfbr" value="subtracks-encodeYaleChipRfbr">
+        <option name="Yale ChIP RFBR" value="encodeYaleChipRfbr"/>
+        <option name="Yale RFBR Clusters" value="encodeYaleChipRfbrClusters"/>
+        <option name="Yale RFBR Deserts" value="encodeYaleChipRfbrDeserts"/>
+      </option>
+      <option name="encodeSangerChip" value="subtracks-encodeSangerChip">
+        <option name="Sanger ChIP" value="encodeSangerChip"/>
+        <option name="SI CTCF GM06990" value="encodeSangerChipCTCF"/>
+        <option name="SI H3K27me3 GM06990" value="encodeSangerChipH3K27me3"/>
+        <option name="SI H3K36me3 GM06990" value="encodeSangerChipH3K36me3"/>
+        <option name="SI H3K4m1 GM6990" value="encodeSangerChipH3K4me1"/>
+        <option name="SI H3K4me1 HFL-1" value="encodeSangerChipH3K4me1HFL1"/>
+        <option name="SI H3K4me1 HeLa" value="encodeSangerChipH3K4me1HeLa"/>
+        <option name="SI H3K4me1 MOLT4" value="encodeSangerChipH3K4me1Molt4"/>
+        <option name="SI H3K4me1 PTR8" value="encodeSangerChipH3K4me1Ptr8"/>
+        <option name="SI H3K4m2 GM6990" value="encodeSangerChipH3K4me2"/>
+        <option name="SI H3K4me2 HFL-1" value="encodeSangerChipH3K4me2HFL1"/>
+        <option name="SI H3K4me2 HeLa" value="encodeSangerChipH3K4me2HeLa"/>
+        <option name="SI H3K4me2 K562" value="encodeSangerChipH3K4me2K562"/>
+        <option name="SI H3K4me2 MOLT4" value="encodeSangerChipH3K4me2Molt4"/>
+        <option name="SI H3K4me2 PTR8" value="encodeSangerChipH3K4me2Ptr8"/>
+        <option name="SI H3K4m3 GM6990" value="encodeSangerChipH3K4me3"/>
+        <option name="SI H3K4me3 HFL-1" value="encodeSangerChipH3K4me3HFL1"/>
+        <option name="SI H3K4me3 HeLa" value="encodeSangerChipH3K4me3HeLa"/>
+        <option name="SI H3K4me3 K562" value="encodeSangerChipH3K4me3K562"/>
+        <option name="SI H3K4me3 MOLT4" value="encodeSangerChipH3K4me3Molt4"/>
+        <option name="SI H3K4me3 PTR8" value="encodeSangerChipH3K4me3Ptr8"/>
+        <option name="SI H3K79me3 GM06990" value="encodeSangerChipH3K79me3"/>
+        <option name="SI H3K9me3 GM06990" value="encodeSangerChipH3K9me3"/>
+        <option name="SI H3ac GM06990" value="encodeSangerChipH3ac"/>
+        <option name="SI H3ac HFL-1" value="encodeSangerChipH3acHFL1"/>
+        <option name="SI H3ac HeLa" value="encodeSangerChipH3acHeLa"/>
+        <option name="SI H3ac K562" value="encodeSangerChipH3acK562"/>
+        <option name="SI H3ac MOLT4" value="encodeSangerChipH3acMolt4"/>
+        <option name="SI H4ac GM06990" value="encodeSangerChipH4ac"/>
+        <option name="SI H4ac HFL-1" value="encodeSangerChipH4acHFL1"/>
+        <option name="SI H4ac HeLa" value="encodeSangerChipH4acHeLa"/>
+        <option name="SI H4ac K562" value="encodeSangerChipH4acK562"/>
+        <option name="SI H4ac MOLT4" value="encodeSangerChipH4acMolt4"/>
+      </option>
+      <option name="encodeAffyChIpHl60Sites" value="subtracks-encodeAffyChIpHl60Sites">
+        <option name="Affy Sites" value="encodeAffyChIpHl60Sites"/>
+        <option name="Affy Brg1 RA 0h" value="encodeAffyChIpHl60SitesBrg1Hr00"/>
+        <option name="Affy Brg1 RA 2h" value="encodeAffyChIpHl60SitesBrg1Hr02"/>
+        <option name="Affy Brg1 RA 8h" value="encodeAffyChIpHl60SitesBrg1Hr08"/>
+        <option name="Affy Brg1 RA 32h" value="encodeAffyChIpHl60SitesBrg1Hr32"/>
+        <option name="Affy CEBPe RA 0h" value="encodeAffyChIpHl60SitesCebpeHr00"/>
+        <option name="Affy CEBPe RA 2h" value="encodeAffyChIpHl60SitesCebpeHr02"/>
+        <option name="Affy CEBPe RA 8h" value="encodeAffyChIpHl60SitesCebpeHr08"/>
+        <option name="Affy CEBPe RA 32h" value="encodeAffyChIpHl60SitesCebpeHr32"/>
+        <option name="Affy CTCF RA 0h" value="encodeAffyChIpHl60SitesCtcfHr00"/>
+        <option name="Affy CTCF RA 2h" value="encodeAffyChIpHl60SitesCtcfHr02"/>
+        <option name="Affy CTCF RA 8h" value="encodeAffyChIpHl60SitesCtcfHr08"/>
+        <option name="Affy CTCF RA 32h" value="encodeAffyChIpHl60SitesCtcfHr32"/>
+        <option name="Affy H3K27me3 RA 0h" value="encodeAffyChIpHl60SitesH3K27me3Hr00"/>
+        <option name="Affy H3K27me3 RA 2h" value="encodeAffyChIpHl60SitesH3K27me3Hr02"/>
+        <option name="Affy H3K27me3 RA 8h" value="encodeAffyChIpHl60SitesH3K27me3Hr08"/>
+        <option name="Affy H3K27me3 RA 32h" value="encodeAffyChIpHl60SitesH3K27me3Hr32"/>
+        <option name="Affy H4Kac4 RA 0h" value="encodeAffyChIpHl60SitesH4Kac4Hr00"/>
+        <option name="Affy H4Kac4 RA 2h" value="encodeAffyChIpHl60SitesH4Kac4Hr02"/>
+        <option name="Affy H4Kac4 RA 8h" value="encodeAffyChIpHl60SitesH4Kac4Hr08"/>
+        <option name="Affy H4Kac4 RA 32h" value="encodeAffyChIpHl60SitesH4Kac4Hr32"/>
+        <option name="Affy P300 RA 0h" value="encodeAffyChIpHl60SitesP300Hr00"/>
+        <option name="Affy P300 RA 2h" value="encodeAffyChIpHl60SitesP300Hr02"/>
+        <option name="Affy P300 RA 8h" value="encodeAffyChIpHl60SitesP300Hr08"/>
+        <option name="Affy P300 RA 32h" value="encodeAffyChIpHl60SitesP300Hr32"/>
+        <option name="Affy PU1 RA 0h" value="encodeAffyChIpHl60SitesPu1Hr00"/>
+        <option name="Affy PU1 RA 2h" value="encodeAffyChIpHl60SitesPu1Hr02"/>
+        <option name="Affy PU1 RA 8h" value="encodeAffyChIpHl60SitesPu1Hr08"/>
+        <option name="Affy PU1 RA 32h" value="encodeAffyChIpHl60SitesPu1Hr32"/>
+        <option name="Affy RARA RA 0h" value="encodeAffyChIpHl60SitesRaraHr00"/>
+        <option name="Affy RARA RA 2h" value="encodeAffyChIpHl60SitesRaraHr02"/>
+        <option name="Affy RARA RA 8h" value="encodeAffyChIpHl60SitesRaraHr08"/>
+        <option name="Affy RARA RA 32h" value="encodeAffyChIpHl60SitesRaraHr32"/>
+        <option name="Affy Pol2 RA 0h" value="encodeAffyChIpHl60SitesRnapHr00"/>
+        <option name="Affy Pol2 RA 2h" value="encodeAffyChIpHl60SitesRnapHr02"/>
+        <option name="Affy Pol2 RA 8h" value="encodeAffyChIpHl60SitesRnapHr08"/>
+        <option name="Affy Pol2 RA 32h" value="encodeAffyChIpHl60SitesRnapHr32"/>
+        <option name="Affy SIRT1 RA 0h" value="encodeAffyChIpHl60SitesSirt1Hr00"/>
+        <option name="Affy SIRT1 RA 2h" value="encodeAffyChIpHl60SitesSirt1Hr02"/>
+        <option name="Affy SIRT1 RA 8h" value="encodeAffyChIpHl60SitesSirt1Hr08"/>
+        <option name="Affy SIRT1 RA 32h" value="encodeAffyChIpHl60SitesSirt1Hr32"/>
+        <option name="Affy TFIIB RA 32h" value="encodeAffyChIpHl60SitesTfiibHr32"/>
+      </option>
+        <option name="Yale ChIP" value="encodeYaleChipSuper"/>
+      <option name="encodeUcsdNgGif" value="subtracks-encodeUcsdNgGif">
+        <option name="LI Ng gIF ChIP" value="encodeUcsdNgGif"/>
+        <option name="LI H3ac -gIF" value="encodeUcsdNgHeLaAcH3_p0"/>
+        <option name="LI H3ac -gIF Pk" value="encodeUcsdNgHeLaAcH3_p0_peak"/>
+        <option name="LI H3ac +gIF" value="encodeUcsdNgHeLaAcH3_p30"/>
+        <option name="LI H3ac +gIF Pk" value="encodeUcsdNgHeLaAcH3_p30_peak"/>
+        <option name="LI H4ac -gIF" value="encodeUcsdNgHeLaAcH4_p0"/>
+        <option name="LI H4ac -gIF Pk" value="encodeUcsdNgHeLaAcH4_p0_peak"/>
+        <option name="LI H3K4me2 -gIF" value="encodeUcsdNgHeLaDmH3K4_p0"/>
+        <option name="LI H3K4m2 -IF Pk" value="encodeUcsdNgHeLaDmH3K4_p0_peak"/>
+        <option name="LI H3K4me2 +gIF" value="encodeUcsdNgHeLaDmH3K4_p30"/>
+        <option name="LI H3K4m2 +IF Pk" value="encodeUcsdNgHeLaDmH3K4_p30_peak"/>
+        <option name="LI H3K4me3 -gIF" value="encodeUcsdNgHeLaH3K4me3_p0"/>
+        <option name="LI H3K4m3 +gIF" value="encodeUcsdNgHeLaH3K4me3_p30"/>
+        <option name="LI Pol2 -gIF" value="encodeUcsdNgHeLaRnap_p0"/>
+        <option name="LI Pol2 +gIF" value="encodeUcsdNgHeLaRnap_p30"/>
+        <option name="LI STAT1 +gIF" value="encodeUcsdNgHeLaStat1_p30"/>
+        <option name="LI STAT1 +gIF Pk" value="encodeUcsdNgHeLaStat1_p30_peak"/>
+      </option>
+      <option name="encodeYaleChipPval" value="subtracks-encodeYaleChipPval">
+        <option name="Yale ChIP pVal" value="encodeYaleChipPval"/>
+        <option name="YU BAF155 HeLa P" value="encodeYaleChipPvalBaf155"/>
+        <option name="YU BAF155 K562 P" value="encodeYaleChipPvalBaf155K562"/>
+        <option name="YU BAF170 HeLa P" value="encodeYaleChipPvalBaf170"/>
+        <option name="YU BAF170 K562 P" value="encodeYaleChipPvalBaf170K562"/>
+        <option name="YU BAF47 K562 P" value="encodeYaleChipPvalBaf47K562"/>
+        <option name="YU c-Fos HeLa P" value="encodeYaleChipPvalFos"/>
+        <option name="YU H3K27me3 HeLa P" value="encodeYaleChipPvalH3k27me3Hela"/>
+        <option name="YU H4Kac4 GM P" value="encodeYaleChipPvalH4kac4Gm06990"/>
+        <option name="YU H4Kac4 HeLa P" value="encodeYaleChipPvalH4kac4Hela"/>
+        <option name="YU c-Jun HeLa P" value="encodeYaleChipPvalJun"/>
+        <option name="YU NRSF HeLa P" value="encodeYaleChipPvalNrsfHela"/>
+        <option name="YU P65-C HeLa TNF P" value="encodeYaleChipPvalP65cHelaTnfa"/>
+        <option name="YU P65-N HeLa TNF P" value="encodeYaleChipPvalP65nHelaTnfa"/>
+        <option name="YU Pol2 GM P" value="encodeYaleChipPvalPol2Gm06990"/>
+        <option name="YU Pol2 HeLa P" value="encodeYaleChipPvalPol2Hela"/>
+        <option name="YU Pol2N GM P" value="encodeYaleChipPvalPol2nGm06990"/>
+        <option name="YU Pol2N HeLa P" value="encodeYaleChipPvalPol2nHela"/>
+        <option name="YU SMARCA4 HeLa P" value="encodeYaleChipPvalSmarca4Hela"/>
+        <option name="YU SMARCA6 HeLa P" value="encodeYaleChipPvalSmarca6Hela"/>
+        <option name="YU STAT1 HeLa IF P" value="encodeYaleChipPvalStat1HelaIfna"/>
+        <option name="YU TAF1 HeLa P" value="encodeYaleChipPvalTaf"/>
+      </option>
+        <option name="UT-Austin ChIP" value="encodeUtexChipSuper"/>
+      <option name="encodeAffyChIpHl60PvalStrict" value="subtracks-encodeAffyChIpHl60PvalStrict">
+        <option name="Affy Strict pVal" value="encodeAffyChIpHl60PvalStrict"/>
+        <option name="Affy H3K9ac2 0h" value="encodeAffyChIpHl60PvalStrictH3K9K14DHr00"/>
+        <option name="Affy H3K9ac2 2h" value="encodeAffyChIpHl60PvalStrictH3K9K14DHr02"/>
+        <option name="Affy H3K9ac2 8h" value="encodeAffyChIpHl60PvalStrictH3K9K14DHr08"/>
+        <option name="Affy H3K9ac2 32h" value="encodeAffyChIpHl60PvalStrictH3K9K14DHr32"/>
+        <option name="Affy H4Kac4 0h" value="encodeAffyChIpHl60PvalStrictHisH4Hr00"/>
+        <option name="Affy H4Kac4 2h" value="encodeAffyChIpHl60PvalStrictHisH4Hr02"/>
+        <option name="Affy H4Kac4 8h" value="encodeAffyChIpHl60PvalStrictHisH4Hr08"/>
+        <option name="Affy H4Kac4 32h" value="encodeAffyChIpHl60PvalStrictHisH4Hr32"/>
+        <option name="Affy Pol2 0h" value="encodeAffyChIpHl60PvalStrictPol2Hr00"/>
+        <option name="Affy Pol2 2h" value="encodeAffyChIpHl60PvalStrictPol2Hr02"/>
+        <option name="Affy Pol2 8h" value="encodeAffyChIpHl60PvalStrictPol2Hr08"/>
+        <option name="Affy Pol2 32h" value="encodeAffyChIpHl60PvalStrictPol2Hr32"/>
+        <option name="Affy p63 ME-180+" value="encodeAffyChIpHl60PvalStrictp63_ActD"/>
+        <option name="Affy p63 ME-180" value="encodeAffyChIpHl60PvalStrictp63_mActD"/>
+      </option>
+        <option name="UC Davis ChIP" value="encodeUcDavisChipSuper"/>
+      <option name="encodeYaleChIPSTAT1Sig" value="subtracks-encodeYaleChIPSTAT1Sig">
+        <option name="Yale LI Sig" value="encodeYaleChIPSTAT1HeLaBingRenSig"/>
+        <option name="Yale 36-36 Sig" value="encodeYaleChIPSTAT1HeLaMaskLess36mer36bpSig"/>
+        <option name="Yale 50-38 Sig" value="encodeYaleChIPSTAT1HeLaMaskLess50mer38bpSig"/>
+        <option name="Yale 50-50 Sig" value="encodeYaleChIPSTAT1HeLaMaskLess50mer50bpSig"/>
+        <option name="Yale STAT1 Sig" value="encodeYaleChIPSTAT1Sig"/>
+      </option>
+      <option name="encodeUCDavisChip" value="subtracks-encodeUCDavisChip">
+        <option name="UCD Ng ChIP" value="encodeUCDavisChip"/>
+        <option name="UCD C-Myc" value="encodeUCDavisChipMyc"/>
+        <option name="UCD E2F1" value="encodeUCDavisE2F1Median"/>
+        <option name="UCD PolII_GM" value="encodeUCDavisPolIIGM"/>
+        <option name="UCD PolII_HelaS3" value="encodeUCDavisPolIIHelaS3"/>
+        <option name="UCD Taf_GM" value="encodeUCDavisTafGM"/>
+        <option name="UCD Taf_HelaS3" value="encodeUCDavisTafHelaS3"/>
+      </option>
+      <option name="encodeSangerChipHits" value="subtracks-encodeSangerChipHits">
+        <option name="SI H3K4m1 GM6990" value="encodeSangerChipHitH3K4me1GM06990"/>
+        <option name="SI H3K4me1 HeLa" value="encodeSangerChipHitH3K4me1HeLa"/>
+        <option name="SI H3K4m2 GM6990" value="encodeSangerChipHitH3K4me2GM06990"/>
+        <option name="SI H3K4me2 HeLa" value="encodeSangerChipHitH3K4me2HeLa"/>
+        <option name="SI H3K4me2 K562" value="encodeSangerChipHitH3K4me2K562"/>
+        <option name="SI H3K4m3 GM6990" value="encodeSangerChipHitH3K4me3GM06990"/>
+        <option name="SI H3K4me3 HeLa" value="encodeSangerChipHitH3K4me3HeLa"/>
+        <option name="SI H3K4me3 K562" value="encodeSangerChipHitH3K4me3K562"/>
+        <option name="SI H3ac GM06990" value="encodeSangerChipHitH3acGM06990"/>
+        <option name="SI H3ac HeLa" value="encodeSangerChipHitH3acHeLa"/>
+        <option name="SI H3ac K562" value="encodeSangerChipHitH3acK562"/>
+        <option name="SI H4ac GM06990" value="encodeSangerChipHitH4acGM06990"/>
+        <option name="SI H4ac HeLa" value="encodeSangerChipHitH4acHeLa"/>
+        <option name="SI H4ac K562" value="encodeSangerChipHitH4acK562"/>
+        <option name="Sanger ChIP Hits" value="encodeSangerChipHits"/>
+      </option>
+        <option name="LI/UCSD ChIP" value="encodeUcsdChipSuper"/>
+    </option>
+    <option name="ENCODE Chromosome, Chromatin and DNA Structure" value="group-encodeChrom">
+        <option name="BU ORChID" value="encodeBUORChID"/>
+      <option name="encodeUncFaire" value="subtracks-encodeUncFaire">
+        <option name="UNC FAIRE" value="encodeUncFaire"/>
+        <option name="FAIRE Signal" value="encodeUncFaireSignal"/>
+      </option>
+      <option name="encodeUvaDnaRepOrigins" value="subtracks-encodeUvaDnaRepOrigins">
+        <option name="UVa DNA Rep Ori" value="encodeUvaDnaRepOrigins"/>
+        <option name="UVa Ori-Bubble HeLa" value="encodeUvaDnaRepOriginsBubbleHela"/>
+        <option name="UVa Ori-NS GM" value="encodeUvaDnaRepOriginsNSGM"/>
+        <option name="UVa Ori-NS HeLa" value="encodeUvaDnaRepOriginsNSHela"/>
+        <option name="UVa Ori-TR50 HeLa" value="encodeUvaDnaRepOriginsTR50Hela"/>
+      </option>
+        <option name="UVa DNA Rep TR50" value="encodeUvaDnaRepTr50"/>
+        <option name="UVa DNA Rep" value="encodeUvaDnaRepSuper"/>
+      <option name="encodeUvaDnaRepSeg" value="subtracks-encodeUvaDnaRepSeg">
+        <option name="UVa DNA Rep Early" value="encodeUvaDnaRepEarly"/>
+        <option name="UVa DNA Rep Late" value="encodeUvaDnaRepLate"/>
+        <option name="UVa DNA Rep Mid" value="encodeUvaDnaRepMid"/>
+        <option name="UVa DNA Rep PanS" value="encodeUvaDnaRepPanS"/>
+        <option name="UVa DNA Rep Seg" value="encodeUvaDnaRepSeg"/>
+      </option>
+      <option name="encodeRegulomeDnaseArray" value="subtracks-encodeRegulomeDnaseArray">
+        <option name="UW DNase-array" value="encodeRegulomeDnaseArray"/>
+        <option name="DnaseI Sens" value="encodeRegulomeDnaseGM06990Sens"/>
+      </option>
+        <option name="UW DNase" value="encodeUwDnaseSuper"/>
+      <option name="encodeUWRegulomeBase" value="subtracks-encodeUWRegulomeBase">
+        <option name="UW DNase-QCP" value="encodeUWRegulomeBase"/>
+        <option name="CD4" value="encodeUWRegulomeBaseCD4"/>
+        <option name="CaCo2" value="encodeUWRegulomeBaseCaCo2"/>
+        <option name="CaLU3" value="encodeUWRegulomeBaseCaLU3"/>
+        <option name="EryAdult" value="encodeUWRegulomeBaseEryAdult"/>
+        <option name="EryFetal" value="encodeUWRegulomeBaseEryFetal"/>
+        <option name="GM" value="encodeUWRegulomeBaseGM"/>
+        <option name="HMEC" value="encodeUWRegulomeBaseHMEC"/>
+        <option name="HRE" value="encodeUWRegulomeBaseHRE"/>
+        <option name="HeLa" value="encodeUWRegulomeBaseHeLa"/>
+        <option name="HepG2" value="encodeUWRegulomeBaseHepG2"/>
+        <option name="Huh7" value="encodeUWRegulomeBaseHuh7"/>
+        <option name="K562" value="encodeUWRegulomeBaseK562"/>
+        <option name="NHBE" value="encodeUWRegulomeBaseNHBE"/>
+        <option name="PANC" value="encodeUWRegulomeBasePANC"/>
+        <option name="SAEC" value="encodeUWRegulomeBaseSAEC"/>
+        <option name="SKnSH" value="encodeUWRegulomeBaseSKnSH"/>
+      </option>
+      <option name="encodeNhgriDukeDnaseHs" value="subtracks-encodeNhgriDukeDnaseHs">
+        <option name="DNase CD4 Raw" value="encodeNhgriDnaseHsChipRawCd4"/>
+        <option name="DNase GM069 Raw" value="encodeNhgriDnaseHsChipRawGm06990"/>
+        <option name="DNase H9 Raw" value="encodeNhgriDnaseHsChipRawH9"/>
+        <option name="DNase HeLa Raw" value="encodeNhgriDnaseHsChipRawHela"/>
+        <option name="DNase HepG2 Raw" value="encodeNhgriDnaseHsChipRawHepG2"/>
+        <option name="DNase IMR90 Raw" value="encodeNhgriDnaseHsChipRawImr90"/>
+        <option name="DNase K562 Raw" value="encodeNhgriDnaseHsChipRawK562"/>
+        <option name="Duke/NHGRI DNase" value="encodeNhgriDukeDnaseHs"/>
+      </option>
+      <option name="encodeUvaDnaRep" value="subtracks-encodeUvaDnaRep">
+        <option name="UVa DNA Rep" value="encodeUvaDnaRep"/>
+        <option name="UVa DNA Rep 0h" value="encodeUvaDnaRep0"/>
+        <option name="UVa DNA Rep 2h" value="encodeUvaDnaRep2"/>
+        <option name="UVa DNA Rep 4h" value="encodeUvaDnaRep4"/>
+        <option name="UVa DNA Rep 6h" value="encodeUvaDnaRep6"/>
+        <option name="UVa DNA Rep 8h" value="encodeUvaDnaRep8"/>
+      </option>
+    </option>
+    <option name="ENCODE Regions and Genes" value="group-encodeGenes">
+      <option name="encodeGencodeGeneMar07" value="subtracks-encodeGencodeGeneMar07">
+        <option name="Gencode Ref" value="encodeGencodeGeneKnownMar07"/>
+        <option name="Gencode Genes Mar07" value="encodeGencodeGeneMar07"/>
+        <option name="Gencode Polymorph" value="encodeGencodeGenePolymorphicMar07"/>
+        <option name="Gencode Pseudo" value="encodeGencodeGenePseudoMar07"/>
+        <option name="Gencode Putative" value="encodeGencodeGenePutativeMar07"/>
+      </option>
+        <option name="Vienna RNAz" value="encodeUViennaRnaz"/>
+        <option name="Gencode Genes" value="encodeGencodeSuper"/>
+        <option name="EGASP" value="encodeEgaspSuper"/>
+      <option name="encodeGencodeRaceFrags" value="subtracks-encodeGencodeRaceFrags">
+        <option name="Gencode RACEfrags" value="encodeGencodeRaceFrags"/>
+        <option name="RACEfrags Brain" value="encodeGencodeRaceFragsBrain"/>
+        <option name="RACEfrags Colon" value="encodeGencodeRaceFragsColon"/>
+        <option name="RACEfrags GM06990" value="encodeGencodeRaceFragsGM06990"/>
+        <option name="RACEfrags HL60" value="encodeGencodeRaceFragsHL60"/>
+        <option name="RACEfrags Heart" value="encodeGencodeRaceFragsHeart"/>
+        <option name="RACEfrags HeLaS3" value="encodeGencodeRaceFragsHela"/>
+        <option name="RACEfrags Kidney" value="encodeGencodeRaceFragsKidney"/>
+        <option name="RACEfrags Liver" value="encodeGencodeRaceFragsLiver"/>
+        <option name="RACEfrags Lung" value="encodeGencodeRaceFragsLung"/>
+        <option name="RACEfrags Muscle" value="encodeGencodeRaceFragsMuscle"/>
+        <option name="RACEfrags Placenta" value="encodeGencodeRaceFragsPlacenta"/>
+        <option name="RACEfrags Primer" value="encodeGencodeRaceFragsPrimer"/>
+        <option name="RACEfrags Sm Int" value="encodeGencodeRaceFragsSmallIntest"/>
+        <option name="RACEfrags Spleen" value="encodeGencodeRaceFragsSpleen"/>
+        <option name="RACEfrags Stomach" value="encodeGencodeRaceFragsStomach"/>
+        <option name="RACEfrags Testis" value="encodeGencodeRaceFragsTestis"/>
+      </option>
+        <option name="Known+Pred RNA" value="encodeRna"/>
+      <option name="encodeEgaspFull" value="subtracks-encodeEgaspFull">
+        <option name="EGASP Full" value="encodeEgaspFull"/>
+        <option name="AceView" value="encodeEgaspFullAceview"/>
+        <option name="DOGFISH-C" value="encodeEgaspFullDogfish"/>
+        <option name="Ensembl" value="encodeEgaspFullEnsembl"/>
+        <option name="Ensembl Pseudo" value="encodeEgaspFullEnsemblPseudo"/>
+        <option name="Exogean" value="encodeEgaspFullExogean"/>
+        <option name="ExonHunter" value="encodeEgaspFullExonhunter"/>
+        <option name="Fgenesh++" value="encodeEgaspFullFgenesh"/>
+        <option name="GeneID" value="encodeEgaspFullGeneId"/>
+        <option name="GeneID U12" value="encodeEgaspFullGeneIdU12"/>
+        <option name="GeneMark" value="encodeEgaspFullGenemark"/>
+        <option name="Jigsaw" value="encodeEgaspFullJigsaw"/>
+        <option name="Pairgn/NSCAN-E/+" value="encodeEgaspFullPairagonAny"/>
+        <option name="Pairgn/NSCAN-E" value="encodeEgaspFullPairagonMrna"/>
+        <option name="NSCAN" value="encodeEgaspFullPairagonMultiple"/>
+        <option name="SGP2" value="encodeEgaspFullSgp2"/>
+        <option name="SGP2 U12" value="encodeEgaspFullSgp2U12"/>
+        <option name="Fgenesh Pseudo" value="encodeEgaspFullSoftberryPseudo"/>
+        <option name="SPIDA Exons" value="encodeEgaspFullSpida"/>
+        <option name="Twinscan" value="encodeEgaspFullTwinscan"/>
+      </option>
+      <option name="encodeGencodeGeneOct05" value="subtracks-encodeGencodeGeneOct05">
+        <option name="Gencode Ref" value="encodeGencodeGeneKnownOct05"/>
+        <option name="Gencode Genes Oct05" value="encodeGencodeGeneOct05"/>
+        <option name="Gencode Pseudo" value="encodeGencodeGenePseudoOct05"/>
+        <option name="Gencode Putative" value="encodeGencodeGenePutativeOct05"/>
+      </option>
+        <option name="Gencode Introns Oct05" value="encodeGencodeIntronOct05"/>
+      <option name="encodePseudogene" value="subtracks-encodePseudogene">
+        <option name="Pseudogenes" value="encodePseudogene"/>
+        <option name="Consensus Pseudogenes" value="encodePseudogeneConsensus"/>
+        <option name="GIS Pseudogenes" value="encodePseudogeneGIS"/>
+        <option name="Havana-Gencode Pseudogenes" value="encodePseudogeneHavana"/>
+        <option name="UCSC Retrogenes" value="encodePseudogeneUcsc"/>
+        <option name="UCSC Pseudogenes" value="encodePseudogeneUcsc2"/>
+        <option name="Yale Pseudogenes" value="encodePseudogeneYale"/>
+      </option>
+        <option name="ENCODE Regions" value="encodeRegions"/>
+      <option name="encodeEgaspUpdate" value="subtracks-encodeEgaspUpdate">
+        <option name="Augustus Update" value="encodeEgaspUpdAugustusAbinitio"/>
+        <option name="August/EST/Ms Upd" value="encodeEgaspUpdAugustusAny"/>
+        <option name="August/Mouse Upd" value="encodeEgaspUpdAugustusDual"/>
+        <option name="Augustus/EST Upd" value="encodeEgaspUpdAugustusEst"/>
+        <option name="Exogean Update" value="encodeEgaspUpdExogean"/>
+        <option name="FGenesh++ Upd" value="encodeEgaspUpdFgenesh"/>
+        <option name="GeneID Update" value="encodeEgaspUpdGeneId"/>
+        <option name="GeneID U12 Upd" value="encodeEgaspUpdGeneIdU12"/>
+        <option name="Jigsaw Update" value="encodeEgaspUpdJigsaw"/>
+        <option name="SGP2 Update" value="encodeEgaspUpdSgp2"/>
+        <option name="SGP2 U12 Update" value="encodeEgaspUpdSgp2U12"/>
+        <option name="Yale Pseudo Upd" value="encodeEgaspUpdYalePseudo"/>
+        <option name="EGASP Update" value="encodeEgaspUpdate"/>
+      </option>
+      <option name="encodeEgaspPartial" value="subtracks-encodeEgaspPartial">
+        <option name="ACEScan Cons Alt" value="encodeEgaspPartAceCons"/>
+        <option name="ACEScan Other" value="encodeEgaspPartAceOther"/>
+        <option name="Augustus" value="encodeEgaspPartAugustusAbinitio"/>
+        <option name="Augustus/EST/Mouse" value="encodeEgaspPartAugustusAny"/>
+        <option name="Augustus/Mouse" value="encodeEgaspPartAugustusDual"/>
+        <option name="Augustus/EST" value="encodeEgaspPartAugustusEst"/>
+        <option name="GeneZilla" value="encodeEgaspPartGenezilla"/>
+        <option name="SAGA" value="encodeEgaspPartSaga"/>
+        <option name="EGASP Partial" value="encodeEgaspPartial"/>
+      </option>
+    </option>
+  </options>
+</filter>
Index: galaxy-central/tool-data/blastdb.loc
===================================================================
--- galaxy-central/tool-data/blastdb.loc (revision 3)
+++ galaxy-central/tool-data/blastdb.loc (revision 3)
@@ -0,0 +1,32 @@
+#This is a sample file distributed with Galaxy that is used to define a
+#list of nucelotide BLAST databases, using two columns tab separated:
+#
+#<database caption>     <path to base name>
+#
+#The captions typically contain spaces and might end with the build date.
+#It is important that the actual database name does not have a space in it,
+#and that the first tab that appears in the line is right before the path.
+#
+#So, for example, if your database is nt and the path to your base name 
+#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry 
+#would look like this:
+#
+#nt 02 Dec 2009      /depot/data2/galaxy/blastdb/nt/nt.chunk
+#
+#and your /depot/data2/galaxy/blastdb/nt directory would contain all of 
+#your "base names" (e.g.):
+#
+#-rw-r--r--  1 wychung galaxy  23437408 2008-04-09 11:26 nt.chunk.00.nhr
+#-rw-r--r--  1 wychung galaxy   3689920 2008-04-09 11:26 nt.chunk.00.nin
+#-rw-r--r--  1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq
+#...etc...
+#
+#Your blastdb.loc file should include an entry per line for each "base name" 
+#you have stored.  For example:
+#
+#nt 02 Dec 2009	/depot/data2/galaxy/blastdb/nt/nt.chunk
+#wgs 30 Nov 2009	/depot/data2/galaxy/blastdb/wgs/wgs.chunk
+#test 20 Sep 2008	/depot/data2/galaxy/blastdb/test/test
+#...etc...
+#
+#See also blastdb_p.loc which is for any protein BLAST database.
Index: galaxy-central/tool-data/sam_fa_indices.loc
===================================================================
--- galaxy-central/tool-data/sam_fa_indices.loc (revision 3)
+++ galaxy-central/tool-data/sam_fa_indices.loc (revision 3)
@@ -0,0 +1,28 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a sam_fa_indices.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The sam_fa_indices.loc 
+#file has this format (white space characters are TAB characters):
+#
+#index	<seq>	<location>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/depot/data2/galaxy/sam/, 
+#then the sam_fa_indices.loc entry would look like this:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#
+#and your /depot/data2/galaxy/sam/ directory
+#would contain hg18.fa and hg18.fa.fai files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
+#
+#Your sam_fa_indices.loc file should include an entry per line for 
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#index	hg19	/depot/data2/galaxy/sam/hg19.fa
Index: galaxy-central/tool-data/encode_datasets.loc
===================================================================
--- galaxy-central/tool-data/encode_datasets.loc (revision 3)
+++ galaxy-central/tool-data/encode_datasets.loc (revision 3)
@@ -0,0 +1,62 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use ENCODE data.  The encode_datasets.loc file has this format 
+#(white space characters are TAB characters):
+#
+#<EncodeGroup>	<build>	<DisplayName>	<UniqueID>	<FullPathToFile>	<Format>
+#             Encode Groups: ShortHandCode = Group
+#                                       CC = chromatin and chromosomes
+#                                       GT = genes and transcripts
+#                                      MSA = multi-species sequence analysis
+#                                       TR = transcription regulation
+#                                      ALD = All Latest Datasets
+#All files are assumbed to be BED.
+#
+#ALD	hg17	Latest Datasets (20051208)	all_latest_datasets.20051208.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051208.bed	bed
+#ALD	hg17	Latest Datasets (20051208) [gencode_partitioned]	all_latest_datasets.20051208.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051208.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20051208) [gencode_partitioned]	all_latest_datasets.20051208.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051208.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20051208)	all_latest_datasets.20051208.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051208.gff	gff
+#ALD	hg17	Latest Datasets (20051209)	all_latest_datasets.20051209.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051209.bed	bed
+#ALD	hg17	Latest Datasets (20051209) [gencode_partitioned]	all_latest_datasets.20051209.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051209.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20051209) [gencode_partitioned]	all_latest_datasets.20051209.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051209.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20051209)	all_latest_datasets.20051209.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051209.gff	gff
+#ALD	hg17	Latest Datasets (20051211)	all_latest_datasets.20051211.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051211.bed	bed
+#ALD	hg17	Latest Datasets (20051211) [gencode_partitioned]	all_latest_datasets.20051211.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051211.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20051211) [gencode_partitioned]	all_latest_datasets.20051211.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051211.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20051211)	all_latest_datasets.20051211.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051211.gff	gff
+#ALD	hg17	Latest Datasets (20051212)	all_latest_datasets.20051212.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051212.bed	bed
+#ALD	hg17	Latest Datasets (20051212) [gencode_partitioned]	all_latest_datasets.20051212.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051212.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20051212) [gencode_partitioned]	all_latest_datasets.20051212.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051212.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20051212)	all_latest_datasets.20051212.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051212.gff	gff
+#ALD	hg17	Latest Datasets (20051214)	all_latest_datasets.20051214.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051214.bed	bed
+#ALD	hg17	Latest Datasets (20051214) [gencode_partitioned]	all_latest_datasets.20051214.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051214.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20051214) [gencode_partitioned]	all_latest_datasets.20051214.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051214.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20051214)	all_latest_datasets.20051214.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051214.gff	gff
+#ALD	hg17	Latest Datasets (20051216)	all_latest_datasets.20051216.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051216.bed	bed
+#ALD	hg17	Latest Datasets (20051216) [gencode_partitioned]	all_latest_datasets.20051216.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051216.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20051216) [gencode_partitioned]	all_latest_datasets.20051216.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051216.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20051216)	all_latest_datasets.20051216.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20051216.gff	gff
+#ALD	hg17	Latest Datasets (20060105)	all_latest_datasets.20060105.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060105.bed	bed
+#ALD	hg17	Latest Datasets (20060105) [gencode_partitioned]	all_latest_datasets.20060105.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060105.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20060105) [gencode_partitioned]	all_latest_datasets.20060105.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060105.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20060105)	all_latest_datasets.20060105.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060105.gff	gff
+#ALD	hg17	Latest Datasets (20060106)	all_latest_datasets.20060106.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060106.bed	bed
+#ALD	hg17	Latest Datasets (20060106) [gencode_partitioned]	all_latest_datasets.20060106.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060106.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20060106) [gencode_partitioned]	all_latest_datasets.20060106.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060106.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20060106)	all_latest_datasets.20060106.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060106.gff	gff
+#ALD	hg17	Latest Datasets (20060116)	all_latest_datasets.20060116.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060116.bed	bed
+#ALD	hg17	Latest Datasets (20060116) [gencode_partitioned]	all_latest_datasets.20060116.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060116.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20060116) [gencode_partitioned]	all_latest_datasets.20060116.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060116.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20060116)	all_latest_datasets.20060116.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060116.gff	gff
+#ALD	hg17	Latest Datasets (20060124)	all_latest_datasets.20060124.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060124.bed	bed
+#ALD	hg17	Latest Datasets (20060124) [gencode_partitioned]	all_latest_datasets.20060124.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060124.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20060124) [gencode_partitioned]	all_latest_datasets.20060124.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060124.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20060124)	all_latest_datasets.20060124.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060124.gff	gff
+#ALD	hg17	Latest Datasets (20060204)	all_latest_datasets.20060204.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060204.bed	bed
+#ALD	hg17	Latest Datasets (20060204) [gencode_partitioned]	all_latest_datasets.20060204.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060204.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20060204) [gencode_partitioned]	all_latest_datasets.20060204.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060204.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20060204)	all_latest_datasets.20060204.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060204.gff	gff
+#ALD	hg17	Latest Datasets (20060206)	all_latest_datasets.20060206.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060206.bed	bed
+#ALD	hg17	Latest Datasets (20060206) [gencode_partitioned]	all_latest_datasets.20060206.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060206.gencode_partitioned.bed	bed
+#ALD	hg17	Latest Datasets (20060206) [gencode_partitioned]	all_latest_datasets.20060206.gencode_partitioned.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060206.gencode_partitioned.gff	gff
+#ALD	hg17	Latest Datasets (20060206)	all_latest_datasets.20060206.gff	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060206.gff	gff
+#ALD	hg17	Latest Datasets (20060209) [gencode_partitioned]	all_latest_datasets.20060209.gencode_partitioned.bed	/depot/data2/galaxy/encode-data/all_latest/all_latest_datasets.20060209.gencode_partitioned.bed	bed
Index: galaxy-central/tool-data/bowtie_indices_color.loc
===================================================================
--- galaxy-central/tool-data/bowtie_indices_color.loc (revision 3)
+++ galaxy-central/tool-data/bowtie_indices_color.loc (revision 3)
@@ -0,0 +1,31 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of colorspace Bowtie indexed sequences data files.  
+#You will need to create these data files and then create a 
+#bowtie_indices_color.loc file similar to this one (store it in this 
+#directory) that points to the directories in which those files are 
+#stored. The bowtie_indices_color.loc file has this format (white 
+#space characters are TAB characters):
+#
+#<build>	<file_base>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/depot/data2/galaxy/bowtie/hg18/, 
+#then the bowtie_indices_color.loc entry would look like this:
+#
+#hg18	/depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 gh18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices_color.loc file should include an entry per line 
+#for each index set you have stored.  The "file" in the path does not 
+#actually exist, but it is the prefix for the actual index files. For 
+#example:
+#
+#hg18	/depot/data2/galaxy/bowtie/hg18/hg18
+#hg19	/depot/data2/galaxy/bowtie/hg19/hg19
Index: galaxy-central/tool-data/maf_index.loc
===================================================================
--- galaxy-central/tool-data/maf_index.loc (revision 3)
+++ galaxy-central/tool-data/maf_index.loc (revision 3)
@@ -0,0 +1,17 @@
+#This is a sample file distributed with Galaxy that is used by some
+#alignment tools.  The maf_index.loc file has this format (white space 
+#characters are TAB characters):
+#
+#<Display_name UID>	<indexed_for:build1,build2,build3>	<exists_in_maf:build1,build2,build3>	<Comma_Separated_List_of_Full_Paths_To_Files>
+#
+#ENCODE TBA (hg17)	ENCODE_TBA_hg17	armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2	armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2	/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm001/human.ENm001.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm002/human.ENm002.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm003/human.ENm003.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm004/human.ENm004.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm005/human.ENm005.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm006/human.ENm006.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm007/human.ENm007.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm008/human.ENm008.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm009/human.ENm009.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm010/human.ENm010.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm011/human.ENm011.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm012/human.ENm012.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm013/human.ENm013.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm014/human.ENm014.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr111/human.ENr111.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr112/human.ENr112.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr113/human.ENr113.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr114/human.ENr114.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr121/human.ENr121.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr122/human.ENr122.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr123/human.ENr123.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr131/human.ENr131.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr132/human.ENr132.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr133/human.ENr133.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr211/human.ENr211.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr212/human.ENr212.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr213/human.ENr213.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr221/human.ENr221.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr222/human.ENr222.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr223/human.ENr223.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr231/human.ENr231.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr232/human.ENr232.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr233/human.ENr233.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr311/human.ENr311.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr312/human.ENr312.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr313/human.ENr313.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr321/human.ENr321.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr322/human.ENr322.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr323/human.ENr323.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr324/human.ENr324.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr331/human.ENr331.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr332/human.ENr332.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr333/human.ENr333.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr334/human.ENr334.maf
+#ENCODE MAVID (hg17)	ENCODE_MAVID_hg17	armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2	armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2	/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm001.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm002.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm003.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm004.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm005.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm006.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm007.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm008.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm009.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm010.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm011.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm012.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm013.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm014.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr111.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr112.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr113.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr114.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr121.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr122.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr123.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr131.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr132.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr133.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr211.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr212.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr213.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr221.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr222.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr223.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr231.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr232.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr233.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr311.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr312.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr313.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr321.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr322.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr323.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr324.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr331.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr332.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr333.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr334.maf
+#ENCODE TBA (hg16)	ENCODE_TBA_hg16	armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant=elephant,fr1,galago,hedgehog,hg16,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2	armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant=elephant,fr1,galago,hedgehog,hg16,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2	/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm001.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm002.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm003.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm004.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm005.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm006.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm007.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm008.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm009.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm010.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm011.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm012.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm013.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm014.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr111.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr112.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr113.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr114.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr121.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr122.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr123.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr131.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr132.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr133.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr211.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr212.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr213.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr221.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr222.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr223.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr231.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr232.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr233.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr311.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr312.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr313.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr321.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr322.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr323.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr324.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr331.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr332.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr333.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr334.maf
+#8-way multiZ (hg17)	8_WAY_MULTIZ_hg17	canFam1,danRer1,fr1,galGal2,hg17,mm5,panTro1,rn3	canFam1,danRer1,fr1,galGal2,hg17,mm5,panTro1,rn3	/depot/data2/galaxy/hg17/align/8way-multiZ/chr1.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr10.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr11.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr12.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr12_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr13.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr14.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr15.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr16.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr17.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr18.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr19.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr2.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr20.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr21.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr22.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr3.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr4.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr5.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_hla_hap1.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_hla_hap2.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr7.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr8.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr9.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrM.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrX.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrY.maf
+#17-way multiZ (hg18)	17_WAY_MULTIZ_hg18	hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1	hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1	/depot/data2/galaxy/hg18/align/17way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrY.maf
+#3-way multiZ (hg18,panTro2,rheMac2)	3_WAY_MULTIZ_hg18	hg18,panTro2,rheMac2	hg18,panTro2,rheMac2	/depot/data2/galaxy/hg18/align/3way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrY.maf
+#5-way multiZ (hg18,panTro2,rheMac2,mm8,canFam2)	5_WAY_MULTIZ_hg18	hg18,panTro2,rheMac2,mm8,canFam2	hg18,panTro2,rheMac2,mm8,canFam2	/depot/data2/galaxy/hg18/align/5way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrY.maf
+#28-way multiZ (hg18)	28_WAY_MULTIZ_hg18	hg18	hg18,dasNov1,otoGar1,felCat3,galGal3,panTro2,bosTau3,canFam2,loxAfr1,xenTro2,fr2,cavPor2,eriEur1,equCab1,anoCar1,oryLat1,mm8,monDom4,ornAna1,oryCun1,rn4,rheMac2,sorAra1,gasAcu1,echTel1,tetNig1,tupBel1,danRer4	/depot/data2/galaxy/hg18/align/multiz28way/chr1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr10.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr10_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr11.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr11_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr12.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr13.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr13_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr14.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr15.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr15_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr16.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr16_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr17.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr17_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr18.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr18_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr19.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr19_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr1_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr2.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr20.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr21.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr21_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22_h2_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr2_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr3.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr3_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr4.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr4_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5_h2_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_cox_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_qbl_hap2.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr7.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr7_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr8.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr8_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr9.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr9_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrM.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrX.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrX_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrY.maf.lzo
+#15-way multiZ (dm2)	15_WAY_MULTIZ_dm2	dm2,droSim1,droSec1,droYak2,droEre2,droAna3,dp4,droPer1,droWil1,droVir3,droMoj3,droGri2,anoGam1,apiMel2,triCas2	dm2,droSim1,droSec1,droYak2,droEre2,droAna3,dp4,droPer1,droWil1,droVir3,droMoj3,droGri2,anoGam1,apiMel2,triCas2	/depot/data2/galaxy/dm2/align/multiz15way/chr2L.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr2R.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr2h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3L.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3R.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr4.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr4h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrM.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrU.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrX.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrXh.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrYh.maf
+#17-way multiZ (mm8)	17_WAY_MULTIZ_mm8	mm8	hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1	/depot/data2/galaxy/mm8/align/multiz17way/chr10.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr10_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr11.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr12.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr13.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr13_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr14.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr15.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr15_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr16.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr17.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr17_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr18.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr19.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr1.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr1_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr2.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr3.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr4.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr5.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr5_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr6.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr7.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr7_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr8.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr8_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr9.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr9_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrM.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrUn_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrX.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrX_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY_random.maf.lzo
+#8-way multiZ (ponAbe2)	8_WAY_MULTIZ_ponAbe2	ponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1	ponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1	/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_h2_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrM.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrUn.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX_random.maf.lzo
Index: galaxy-central/tool-data/liftOver.loc
===================================================================
--- galaxy-central/tool-data/liftOver.loc (revision 3)
+++ galaxy-central/tool-data/liftOver.loc (revision 3)
@@ -0,0 +1,27 @@
+#This is a sample file distributed with Galaxy that is used by the
+#liftOver tools.  The liftOver.loc file has this format (white space 
+#characters are TAB characters):
+#
+#<FromSpecies>	<ToSpecies>	<PathToChainFile>
+#
+#So, for example, if you had the chain file to convert from anoCar1 to galGal3
+#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, 
+#then the liftOver.loc entry would look like this:
+#
+#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+#
+#and your /depot/data2/galaxy/anoCar1/liftOver directory would 
+#contain all of your "chain" files (e.g.):
+#
+#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
+#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
+#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
+#...etc...
+#
+#Your liftOver.loc file should include an entry per line for each build you can
+#convert.  For example:
+#
+#anoCar1	galGal3	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+#anoCar1	gasAcu1	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
+#anoCar1	hg18	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
+#...etc...
Index: galaxy-central/tool-data/shared/ucsc/builds.txt
===================================================================
--- galaxy-central/tool-data/shared/ucsc/builds.txt (revision 3)
+++ galaxy-central/tool-data/shared/ucsc/builds.txt (revision 3)
@@ -0,0 +1,152 @@
+#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn
+?	unspecified (?)
+hg19Haps	hg19Haplotypes Feb. 2009 (GRCh37/hg19Haps) (hg19Haps)
+hg19	Human Feb. 2009 (GRCh37/hg19) (hg19)
+hg18	Human Mar. 2006 (NCBI36/hg18) (hg18)
+hg17	Human May 2004 (NCBI35/hg17) (hg17)
+hg16	Human July 2003 (NCBI34/hg16) (hg16)
+hg15	Human Apr. 2003 (NCBI33/hg15) (hg15)
+venter1	J. Craig Venter Sep. 2007 (HuRef/venter1) (venter1)
+panTro2	Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2)
+panTro1	Chimp Nov. 2003 (CGSC 1.1/panTro1) (panTro1)
+gorGor2	Gorilla Aug. 2009 (Sanger 4/gorGor2) (gorGor2)
+gorGor1	Gorilla Oct. 2008 (Sanger 0.1/gorGor1) (gorGor1)
+ponAbe2	Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2)
+rheMac2	Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2)
+papHam1	Baboon Nov. 2008 (Baylor 1.0/papHam1) (papHam1)
+calJac3	Marmoset March 2009 (WUGSC 3.2/calJac3) (calJac3)
+calJac1	Marmoset June 2007 (WUGSC 2.0.2/calJac1) (calJac1)
+otoGar1	Bushbaby Dec. 2006 (Broad/otoGar1) (otoGar1)
+micMur1	Mouse lemur Jun. 2003 (Broad/micMur1) (micMur1)
+tupBel1	Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1)
+mmtv	MMTV Nov. 2009 (MMTV/mmtv) (mmtv)
+homPan20	chimp/human Jun. 2008 (UCSC Recon/homPan20) (homPan20)
+homIni20	orang/human Jun. 2008 (UCSC Recon/homIni20) (homIni20)
+sorAra1	Shrew June 2006 (Broad/sorAra1) (sorAra1)
+mm9	Mouse July 2007 (NCBI37/mm9) (mm9)
+mm8	Mouse Feb. 2006 (NCBI36/mm8) (mm8)
+mm7	Mouse Aug. 2005 (NCBI35/mm7) (mm7)
+rn4	Rat Nov. 2004 (Baylor 3.4/rn4) (rn4)
+rn3	Rat June 2003 (Baylor 3.1/rn3) (rn3)
+speTri1	Squirrel Feb. 2008 (Broad/speTri1) (speTri1)
+cavPor3	Guinea pig Feb. 2008 (Broad/cavPor3) (cavPor3)
+oryCun2	Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2)
+oryCun1	Rabbit May 2005 (Broad/oryCun1) (oryCun1)
+ochPri2	Pika Jul. 2008 (Broad/ochPri2) (ochPri2)
+eriEur1	Hedgehog June 2006 (Broad/eriEur1) (eriEur1)
+felCatV17e	Cat Dec. 2008 (NHGRI/GTB V17e/felCatV17e) (felCatV17e)
+felCat3	Cat Mar. 2006 (Broad/felCat3) (felCat3)
+ailMel1	Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) (ailMel1)
+nemVec1	Starlet sea anemone Jun. 2007 (JGI-PDF/nemVec1) (nemVec1)
+canFam2	Dog May 2005 (Broad/canFam2) (canFam2)
+canFam1	Dog July 2004 (Broad/canFam1) (canFam1)
+canFamPoodle1	Dog May 2003 (TIGR Poodle/canFamPoodle1) (canFamPoodle1)
+equCab2	Horse Sep. 2007 (Broad/equCab2) (equCab2)
+equCab1	Horse Jan. 2007 (Broad/equCab1) (equCab1)
+susScr2	Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) (susScr2)
+pteVam1	Megabat Jul. 2008 (Broad/pteVam1) (pteVam1)
+myoLuc1	Microbat Mar. 2006 (Broad/myoLuc1) (myoLuc1)
+susScr1	Pig Apr. 2009 (SGSC 9.53/susScr1) (susScr1)
+turTru1	Dolphin Feb. 2008 (Broad/turTru1) (turTru1)
+tarSyr1	Tarsier Aug. 2008 (Broad/tarSyr1) (tarSyr1)
+proCap1	Rock hyrax Jul. 2008 (Broad/proCap1) (proCap1)
+oviAri1	Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) (oviAri1)
+dipOrd1	Kangaroo rat Jul. 2008 (Broad/dipOrd1) (dipOrd1)
+choHof1	Sloth Jul. 2008 (Broad/choHof1) (choHof1)
+bosTau4	Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4)
+bosTau3	Cow Aug. 2006 (Baylor 3.1/bosTau3) (bosTau3)
+bosTau2	Cow Mar. 2005 (Baylor 2.0/bosTau2) (bosTau2)
+macEug1	Wallaby Nov. 2007 (Baylor 1.0/macEug1) (macEug1)
+dasNov2	Armadillo Jul. 2008 (Broad/dasNov2) (dasNov2)
+dasNov1	Armadillo May 2005 (Broad/dasNov1) (dasNov1)
+echTel1	Tenrec July 2005 (Broad/echTel1) (echTel1)
+loxAfr3	Elephant Jul. 2009 (Broad/loxAfr3) (loxAfr3)
+loxAfr2	Elephant Jul. 2008 (Broad/loxAfr2) (loxAfr2)
+loxAfr1	Elephant May 2005 (Broad/loxAfr1) (loxAfr1)
+monDom5	Opossum Oct. 2006 (Broad/monDom5) (monDom5)
+monDom4	Opossum Jan. 2006 (Broad/monDom4) (monDom4)
+monDom1	Opossum Oct. 2004 (Broad prelim/monDom1) (monDom1)
+ornAna1	Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) (ornAna1)
+galGal3	Chicken May 2006 (WUGSC 2.1/galGal3) (galGal3)
+galGal2	Chicken Feb. 2004 (WUGSC 1.0/galGal2) (galGal2)
+taeGut1	Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1)
+anoCar1	Lizard Feb. 2007 (Broad/anoCar1) (anoCar1)
+xenTro2	X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) (xenTro2)
+xenTro1	X. tropicalis Oct. 2004 (JGI 3.0/xenTro1) (xenTro1)
+danRer6	Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6)
+danRer5	Zebrafish July 2007 (Zv7/danRer5) (danRer5)
+danRer4	Zebrafish Mar. 2006 (Zv6/danRer4) (danRer4)
+danRer3	Zebrafish May 2005 (Zv5/danRer3) (danRer3)
+tetNig2	Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) (tetNig2)
+tetNig1	Tetraodon Feb. 2004 (Genoscope 7/tetNig1) (tetNig1)
+fr2	Fugu Oct. 2004 (JGI 4.0/fr2) (fr2)
+fr1	Fugu Aug. 2002 (JGI 3.0/fr1) (fr1)
+gasAcu1	Stickleback Feb. 2006 (Broad/gasAcu1) (gasAcu1)
+oryLat2	Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (oryLat2)
+oryLat1	Medaka Apr. 2006 (NIG/UT MEDAKA1/oryLat1) (oryLat1)
+petMar1	Lamprey Mar. 2007 (WUGSC 3.0/petMar1) (petMar1)
+borEut13	Boreoeutherian Apr. 24. 2006 (UCSC Recon/borEut13) (borEut13)
+canHg12	Boreoeutherian Nov. 19. 2005 (UCSC Recon/canHg12) (canHg12)
+rodEnt13	Rodent Apr. 24. 2006 (UCSC Recon/rodEnt13) (rodEnt13)
+priMat13	Primate Apr. 24. 2006 (UCSC Recon/priMat13) (priMat13)
+nonAfr13	Non-Afrotheria Apr. 24. 2006 (UCSC Recon/nonAfr13) (nonAfr13)
+lauRas13	Laurasiatheria Apr. 24. 2006 (UCSC Recon/lauRas13) (lauRas13)
+homIni14	Hominidae Oct. 1. 2006 (UCSC Recon/homIni14) (homIni14)
+homIni13	Hominidae Apr. 24. 2006 (UCSC Recon/homIni13) (homIni13)
+gliRes13	Glires Apr. 24. 2006 (UCSC Recon/gliRes13) (gliRes13)
+eutHer13	Eutheria Apr. 24. 2006 (UCSC Recon/eutHer13) (eutHer13)
+euaGli13	Euarchontoglires Apr. 24. 2006 (UCSC Recon/euaGli13) (euaGli13)
+catArr1	Catarrhini June 13. 2006 (UCSC Recon/catArr1) (catArr1)
+afrOth13	Afrotheria Apr. 24. 2006 (UCSC Recon/afrOth13) (afrOth13)
+braFlo1	Lancelet Mar. 2006 (JGI 1.0/braFlo1) (braFlo1)
+ci2	C. intestinalis Mar. 2005 (JGI 2.1/ci2) (ci2)
+ci1	C. intestinalis Dec. 2002 (JGI 1.0/ci1) (ci1)
+cioSav2	C. savignyi July 2005 (Sidow Lab 2.0/cioSav2) (cioSav2)
+cioSav1	C. savignyi Apr. 2003 (Broad/cioSav1) (cioSav1)
+strPur2	S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) (strPur2)
+strPur1	S. purpuratus Apr. 2005 (Baylor 1.1/strPur1) (strPur1)
+ce8	C. elegans Jun 2009 (WS204/ce8) (ce8)
+ce7	C. elegans Feb 2009 (WS200/ce7) (ce7)
+aplCal1	Sea hare Sept. 2008 (Broad 2.0/aplCal1) (aplCal1)
+ce6	C. elegans May 2008 (WS190/ce6) (ce6)
+ce5	C. elegans Aug. 2007 (WS180/ce5) (ce5)
+ce4	C. elegans Jan. 2007 (WS170/ce4) (ce4)
+ce3	C. elegans March 2005 (WS140/ce3) (ce3)
+ce2	C. elegans Mar. 2004 (WS120/ce2) (ce2)
+caePb2	C. brenneri Feb. 2008 (WUGSC 6.0.1/caePb2) (caePb2)
+caePb1	C. brenneri Jan. 2007 (WUGSC 4.0/caePb1) (caePb1)
+cb3	C. briggsae Jan. 2007 (WUGSC 1.0/cb3) (cb3)
+cb2	C. briggsae Aug 2005 (WUGSC prelim/cb2) (cb2)
+cb1	C. briggsae July 2002 (WormBase cb25.agp8/cb1) (cb1)
+caeRem3	C. remanei May 2007 (WUGSC 15.0.1/caeRem3) (caeRem3)
+caeRem2	C. remanei Mar. 2006 (WUGSC 1.0/caeRem2) (caeRem2)
+caeRem1	C. remanei March 2005 (WUGSC prelim/caeRem1) (caeRem1)
+caeJap2	C. japonica Jan. 2009 (WUGSC 4.0.1/caeJap2) (caeJap2)
+caeJap1	C. japonica Mar. 2008 (WUGSC 3.0.2/caeJap1) (caeJap1)
+priPac1	P. pacificus Feb. 2007 (WUGSC 5.0/priPac1) (priPac1)
+dm3	D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3)
+dm2	D. melanogaster Apr. 2004 (BDGP R4/dm2) (dm2)
+dm1	D. melanogaster Jan. 2003 (BDGP R3/dm1) (dm1)
+droSim1	D. simulans Apr. 2005 (WUGSC mosaic 1.0/droSim1) (droSim1)
+droSec1	D. sechellia Oct. 2005 (Broad/droSec1) (droSec1)
+droYak2	D. yakuba Nov. 2005 (WUGSC 7.1/droYak2) (droYak2)
+droYak1	D. yakuba Apr. 2004 (WUGSC 1.0/droYak1) (droYak1)
+droEre1	D. erecta Aug. 2005 (Agencourt prelim/droEre1) (droEre1)
+droAna2	D. ananassae Aug. 2005 (Agencourt prelim/droAna2) (droAna2)
+droAna1	D. ananassae July 2004 (TIGR/droAna1) (droAna1)
+dp3	D. pseudoobscura Nov. 2004 (FlyBase 1.03/dp3) (dp3)
+dp2	D. pseudoobscura Aug. 2003 (Baylor freeze1/dp2) (dp2)
+droPer1	D. persimilis Oct. 2005 (Broad/droPer1) (droPer1)
+droVir2	D. virilis Aug. 2005 (Agencourt prelim/droVir2) (droVir2)
+droVir1	D. virilis July 2004 (Agencourt prelim/droVir1) (droVir1)
+droMoj2	D. mojavensis Aug. 2005 (Agencourt prelim/droMoj2) (droMoj2)
+droMoj1	D. mojavensis Aug. 2004 (Agencourt prelim/droMoj1) (droMoj1)
+droGri1	D. grimshawi Aug. 2005 (Agencourt prelim/droGri1) (droGri1)
+anoGam1	A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1)
+apiMel2	A. mellifera Jan. 2005 (Baylor 2.0/apiMel2) (apiMel2)
+apiMel1	A. mellifera July 2004 (Baylor 1.2/apiMel1) (apiMel1)
+triCas2	T. castaneum Sep. 2005 (Baylor 2.0/triCas2) (triCas2)
+falciparum	P. falciparum Plasmodium falciparum (?/falciparum) (falciparum)
+sacCer2	S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)
+sacCer1	S. cerevisiae Oct. 2003 (SGD/sacCer1) (sacCer1)
+sc1	SARS coronavirus Apr. 2003 (GenBank Apr. 14 '03/sc1) (sc1)
Index: galaxy-central/tool-data/annotation_profiler_valid_builds.txt
===================================================================
--- galaxy-central/tool-data/annotation_profiler_valid_builds.txt (revision 3)
+++ galaxy-central/tool-data/annotation_profiler_valid_builds.txt (revision 3)
@@ -0,0 +1,1 @@
+hg18
Index: galaxy-central/tool-data/quality_scores.loc
===================================================================
--- galaxy-central/tool-data/quality_scores.loc (revision 3)
+++ galaxy-central/tool-data/quality_scores.loc (revision 3)
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that is used by some
+#regional variation tools.  The quality_scores.loc file has this format (white 
+#space characters are TAB characters):
+#
+#<build>	<QualityScoreDirectoryPath>
+#
+#So, for example, if you had panTro2 qualit score files stored in 
+#/depot/data2/galaxy/panTro2/quality_scores, then the quality_scores.loc entry 
+#would look like this:
+#
+#panTro2 /depot/data2/galaxy/panTro2/quality_scores
+#
+#and your /depot/data2/galaxy/panTro2/quality_scores directory would 
+#contain all of your quality score files (e.g.):
+#
+#-rw-r--r--  1 gua110 galaxy 10964768 2007-10-02 10:33 chr10.qa.bqv
+#-rw-r--r--  1 gua110 galaxy  1749899 2007-10-02 10:33 chr10_random.qa.bqv
+#-rw-r--r--  1 gua110 galaxy 11310721 2007-10-02 10:33 chr11.qa.bqv
+#...etc...
+#
+#Your quality_scores.loc file should include an entry per line for each quality score 
+#file you have stored.  For example:
+#
+#panTro2	/depot/data2/galaxy/panTro2/quality_scores
+#rheMac2	/depot/data2/galaxy/rheMac2/quality_scores
+#ponAbe2	/depot/data2/galaxy/ponAbe2/quality_scores
Index: galaxy-central/tool-data/twobit.loc
===================================================================
--- galaxy-central/tool-data/twobit.loc (revision 3)
+++ galaxy-central/tool-data/twobit.loc (revision 3)
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that is used by some
+#tools.  The twobit.loc file has this format (white space characters 
+#are TAB characters):
+#
+#<Build>	<FullPathToFile>
+#
+#So, for example, if you had droPer1 twobit files stored in 
+#/depot/data2/galaxy/droPer1/, then the twobit.loc entry 
+#would look like this:
+#
+#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit
+#
+#and your /depot/data2/galaxy/droPer1/ directory would 
+#contain all of your twobit files (e.g.):
+#
+#-rw-rw-r--   1 nate   galaxy 48972650 2007-05-04 11:27 droPer1.2bit
+#...etc...
+#
+#Your twobit.loc file should include an entry per line for each twobit 
+#file you have stored.  For example:
+#
+#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit
+#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit
+#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit
+#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit
+#...etc...
Index: galaxy-central/tool-data/binned_scores.loc
===================================================================
--- galaxy-central/tool-data/binned_scores.loc (revision 3)
+++ galaxy-central/tool-data/binned_scores.loc (revision 3)
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of FileBinnedArray data files.  You will need
+#to create these data files and then create a binned_scores.loc file 
+#similar to this one (store it in this directory ) that points to 
+#the directories in which those files are stored.  The binned_scores.loc 
+#file has this format (white space characters are TAB characters):
+#
+#<build>	<description>	<dir>
+#
+#So, for example, if you had hg16 ENCODE binCons on MLAGAN alignments
+#stored in /depot/data2/galaxy/binned_scores/hg16/encode_bincons_lagan, 
+#then the binned_scores.loc entry would look like this:
+#
+#hg16    ENCODE binCons on MLAGAN alignments     /depot/data2/galaxy/binned_scores/hg16/encode_bincons_lagan
+#
+#and your /depot/data2/galaxy/binned_scores/hg16/encode_bincons_lagan
+#directory would contain all of your "binned" files (e.g.):
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 ENm001
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 ENm002
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 ENm003
+#...etc...
+#
+#Your binned_scores.loc file should include an entry per line for each
+#"binned" file you have stored.  For example:
+#
+#hg16	ENCODE binCons on MLAGAN alignments	/depot/data2/galaxy/binned_scores/hg16/encode_bincons_lagan
+#hg16	ENCODE binCons on TBA alignments	/depot/data2/galaxy/binned_scores/hg16/encode_bincons_tba
+#hg16	ENCODE GERP on MLAGAN alignment	/depot/data2/galaxy/binned_scores/hg16/encode_gerp_lagan
+#hg16	ENCODE GERP on TBA alignment	/depot/data2/galaxy/binned_scores/hg16/encode_gerp_tba
+#hg16	ENCODE phastCons on MLAGAN alignment	/depot/data2/galaxy/binned_scores/hg16/encode_phastcons_lagan
+#hg16	ENCODE phastCons on TBA alignment	/depot/data2/galaxy/binned_scores/hg16/encode_phatcons_tba
+#hg17	ENCODE phastCons on TBA alignment	/depot/data2/galaxy/binned_scores/hg17/phastcons_encode_sep2005_tba
+#hg17	phastCons on 8-species multiz, 16-Jun-2005	/depot/data2/galaxy/binned_scores/hg17/phastcons_mzPt1Mm5Rn3Cf1Gg2Fr1Dr1/
+#hg17	phastCons on 17-species multiz, 13-Apr-2006	/depot/data2/galaxy/binned_scores/hg17/phastCons17way/ba
+#hg17	ESPERR Regulatory Potential, 7-species, 23-Jun-2006	/depot/data2/galaxy/binned_scores/hg17/esperr_rp_7way/ba
+#hg18	phastCons on 17-species multiz, 06-Apr-2006	/depot/data2/galaxy/binned_scores/hg18/phastCons17way/ba
Index: galaxy-central/tool-data/bfast_indexes.loc
===================================================================
--- galaxy-central/tool-data/bfast_indexes.loc (revision 3)
+++ galaxy-central/tool-data/bfast_indexes.loc (revision 3)
@@ -0,0 +1,38 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of BFAST indexed sequences data files.  You will need
+#to create these data files and then create a bfast_indices.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The bfast_indexes.loc 
+#file has this format (white space characters are TAB characters):
+#
+#<unique_id>	<build>	<galaxy format extensions valid1,valid2>	<description>	<bfast_index_directory>
+#
+#
+#So, for example, if you had hg18 indexed for 40+ bp NT reads stored in 
+#/galaxy/data/hg18/bfast_index/nt/40+, 
+#then the bfast_indices.loc entry could look like this:
+#
+#hg18_nt_40+	hg18	fastqsanger	hg18: 40+ bp NT Space reads	/galaxy/data/hg18/bfast_index/nt/40+/hg18.fa
+#
+#and your /depot/data2/galaxy/hg18/bfast/nt/40+ directory
+#would contain hg18.fa.*.brg and hg18.fa.*.bif files:
+#hg18.fa.nt.brg
+#hg18.fa.nt.1.1.bif
+#hg18.fa.nt.2.1.bif
+#...etc...
+#or similarly for color space indexes:
+#hg18.fa.nt.brg #NB: the localalign process requires the nucleotide brg file
+#hg18.fa.cs.brg
+#hg18.fa.cs.1.1.bif
+#hg18.fa.cs.2.1.bif
+#...etc...
+#
+#a 'generic' directory can be used to hold intermixed NT and CS indexes, when differentiating is not needed, the bfast_indices.loc entry could look like this:
+#hg18_standard	hg18	fastqsanger,fastqcssanger	hg18 standard indexes	/galaxy/data/hg18/bfast_index/hg18.fa
+#
+#The use of symlinks to prevent copying of e.g. .fa and .brg files is recommended
+#
+#hg18_nt_40+	hg18	fastqsanger	hg18: 40+ bp NT Space reads	/galaxy/data/hg18/bfast_index/nt/40+/hg18.fa
+#hg18_cs_50+	hg18	fastqcssanger	hg18: 50+ bp Color space reads	/galaxy/data/hg18/bfast_index/cs/50+/hg18.fa
+#hg18_nt_40-	hg18	fastqsanger	hg18: 40- bp NT Space reads	/galaxy/data/hg18/bfast_index/nt/40-/hg18.fa
+#phiX_nt_50	phiX	fastqsanger	phiX: 50 bp NT Space reads	/galaxy/data/phiX/bfast_index/nt/50/phiX.fa
Index: galaxy-central/tool-data/bowtie_indices.loc
===================================================================
--- galaxy-central/tool-data/bowtie_indices.loc (revision 3)
+++ galaxy-central/tool-data/bowtie_indices.loc (revision 3)
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files.  You will need
+#to create these data files and then create a bowtie_indices.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The bowtie_indices.loc 
+#file has this format (white space characters are TAB characters):
+#
+#<build>	<file_base>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/depot/data2/galaxy/bowtie/hg18/, 
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18	/depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 gh18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for 
+#each index set you have stored.  The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files.  For example:
+#
+#hg18	/depot/data2/galaxy/bowtie/hg18/hg18
+#hg19	/depot/data2/galaxy/bowtie/hg19/hg19
Index: galaxy-central/tool-data/phastOdds.loc
===================================================================
--- galaxy-central/tool-data/phastOdds.loc (revision 3)
+++ galaxy-central/tool-data/phastOdds.loc (revision 3)
@@ -0,0 +1,21 @@
+#This is a sample file distributed with Galaxy that is used by the
+#phastOdds scores tool.  The phastOdds.loc file has this format (white space 
+#characters are TAB characters):
+#
+#<build>	<description>	<path to phastOdds score files>
+#
+#So, for example, if you had hg17 ENCODE regions only, SEP-2005 tba.v2 alignments
+#stored in /depot/data2/galaxy/phastOdds_precomputed/encode_SEP-2005_tba.v2_phastOdds, 
+#then the phastOdds.loc entry would look like this:
+#
+#hg17	ENCODE regions only, SEP-2005 tba.v2 alignments	/depot/data2/galaxy/phastOdds_precomputed/encode_SEP-2005_tba.v2_phastOdds
+#
+#and your /depot/data2/galaxy/phastOdds_precomputed/ directory would 
+#contain all of your alignment files (e.g.):
+#
+#-rw-r--r--   1 james g2cache 56555036 2006-02-22 18:26 encode_SEP-2005_tba.v2_phastOdds.h5
+#-rw-r--r--   1 james g2cache     1367 2006-02-08 12:23 encode_SEP-2005_tba.v2_phastOdds.mapping.bed
+#...etc...
+#
+#Your phastOdds.loc file should include an entry per line for each phastOdds 
+#file you have stored.
Index: galaxy-central/tool-data/srma_index.loc
===================================================================
--- galaxy-central/tool-data/srma_index.loc (revision 3)
+++ galaxy-central/tool-data/srma_index.loc (revision 3)
@@ -0,0 +1,25 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of SRMA indexed sequences data files. You will need
+#to create these data files and then create a srma_index.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The srma_index.loc 
+#file has this format (white space is the TAB character):
+#
+#<build>	<fasta_file>
+#
+#So, for example, if you had hg18 indexed and stored in 
+#/depot/data2/galaxy/srma/hg18/, 
+#then the srma_index.loc entry would look like this:
+#
+#hg18	/depot/data2/galaxy/srma/hg18/hg18.fa
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be 
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
Index: galaxy-central/tool-data/microbial_data.loc
===================================================================
--- galaxy-central/tool-data/microbial_data.loc (revision 3)
+++ galaxy-central/tool-data/microbial_data.loc (revision 3)
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to retrieve microbial data via a URL .
+#
+#ORG	campJeju_RM1221_1	Campylobacter jejuni RM1221	bacteria	Epsilonproteobacteria	chr	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=303	UCSC
+#CHR	campJeju_RM1221_1	chr	Campylobacter jejuni RM1221, complete genome	1777831	57236892	None	http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NC_003912
+#DATA	campJeju_RM1221_1_chr_CDS	campJeju_RM1221_1	chr	CDS	bed	/depot/data2/galaxy/microbes/campJeju_RM1221_1/chr.CDS.bed
+#DATA	campJeju_RM1221_1_chr_tRNA	campJeju_RM1221_1	chr	tRNA	bed	/depot/data2/galaxy/microbes/campJeju_RM1221_1/chr.tRNA.bed
+#DATA	campJeju_RM1221_1_chr_rRNA	campJeju_RM1221_1	chr	rRNA	bed	/depot/data2/galaxy/microbes/campJeju_RM1221_1/chr.rRNA.bed
+#DATA	campJeju_RM1221_1_chr_seq	campJeju_RM1221_1	chr	sequence	fasta	/depot/data2/galaxy/microbes/campJeju_RM1221_1/chr.fna
+#DATA	campJeju_RM1221_1_chr_GeneMark	campJeju_RM1221_1	chr	GeneMark	bed	/depot/data2/galaxy/microbes/campJeju_RM1221_1/chr.GeneMark.bed
+#DATA	campJeju_RM1221_1_chr_GeneMarkHMM	campJeju_RM1221_1	chr	GeneMarkHMM	bed	/depot/data2/galaxy/microbes/campJeju_RM1221_1/chr.GeneMarkHMM.bed
+#DATA	campJeju_RM1221_1_chr_Glimmer3	campJeju_RM1221_1	chr	Glimmer3	bed	/depot/data2/galaxy/microbes/campJeju_RM1221_1/chr.Glimmer3.bed
+#ORG	12521	Clostridium perfringens SM101	bacteria	Firmicutes	NC_008262,NC_008263,NC_008264,NC_008265	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521	None
+#CHR	12521	NC_008265	Clostridium perfringens phage phiSM101, complete genome	38092	110804020	None	http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NC_008265
+#DATA	12521_NC_008265_CDS	12521	NC_008265	CDS	bed	/depot/data2/galaxy/microbes/12521/NC_008265.CDS.bed
+#DATA	12521_NC_008265_tRNA	12521	NC_008265	tRNA	bed	/depot/data2/galaxy/microbes/12521/NC_008265.tRNA.bed
+#DATA	12521_NC_008265_rRNA	12521	NC_008265	rRNA	bed	/depot/data2/galaxy/microbes/12521/NC_008265.rRNA.bed
+#DATA	12521_NC_008265_seq	12521	NC_008265	sequence	fasta	/depot/data2/galaxy/microbes/12521/NC_008265.fna
+#DATA	12521_NC_008265_GeneMark	12521	NC_008265	GeneMark	bed	/depot/data2/galaxy/microbes/12521/NC_008265.GeneMark.bed
+#DATA	12521_NC_008265_GeneMarkHMM	12521	NC_008265	GeneMarkHMM	bed	/depot/data2/galaxy/microbes/12521/NC_008265.GeneMarkHMM.bed
+#DATA	12521_NC_008265_Glimmer3	12521	NC_008265	Glimmer3	bed	/depot/data2/galaxy/microbes/12521/NC_008265.Glimmer3.bed
+#CHR	12521	NC_008264	Clostridium perfringens SM101 plasmid 2, complete sequence	12206	110804009	None	http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NC_008264
+#DATA	12521_NC_008264_CDS	12521	NC_008264	CDS	bed	/depot/data2/galaxy/microbes/12521/NC_008264.CDS.bed
+#DATA	12521_NC_008264_tRNA	12521	NC_008264	tRNA	bed	/depot/data2/galaxy/microbes/12521/NC_008264.tRNA.bed
+#DATA	12521_NC_008264_rRNA	12521	NC_008264	rRNA	bed	/depot/data2/galaxy/microbes/12521/NC_008264.rRNA.bed
+#DATA	12521_NC_008264_seq	12521	NC_008264	sequence	fasta	/depot/data2/galaxy/microbes/12521/NC_008264.fna
+#DATA	12521_NC_008264_GeneMark	12521	NC_008264	GeneMark	bed	/depot/data2/galaxy/microbes/12521/NC_008264.GeneMark.bed
+#DATA	12521_NC_008264_GeneMarkHMM	12521	NC_008264	GeneMarkHMM	bed	/depot/data2/galaxy/microbes/12521/NC_008264.GeneMarkHMM.bed
+#DATA	12521_NC_008264_Glimmer3	12521	NC_008264	Glimmer3	bed	/depot/data2/galaxy/microbes/12521/NC_008264.Glimmer3.bed
+#CHR	12521	NC_008263	Clostridium perfringens SM101 plasmid 1, complete sequence	12397	110803998	None	http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NC_008263
+#DATA	12521_NC_008263_CDS	12521	NC_008263	CDS	bed	/depot/data2/galaxy/microbes/12521/NC_008263.CDS.bed
+#DATA	12521_NC_008263_tRNA	12521	NC_008263	tRNA	bed	/depot/data2/galaxy/microbes/12521/NC_008263.tRNA.bed
+#DATA	12521_NC_008263_rRNA	12521	NC_008263	rRNA	bed	/depot/data2/galaxy/microbes/12521/NC_008263.rRNA.bed
+#DATA	12521_NC_008263_seq	12521	NC_008263	sequence	fasta	/depot/data2/galaxy/microbes/12521/NC_008263.fna
+#DATA	12521_NC_008263_GeneMark	12521	NC_008263	GeneMark	bed	/depot/data2/galaxy/microbes/12521/NC_008263.GeneMark.bed
+#DATA	12521_NC_008263_GeneMarkHMM	12521	NC_008263	GeneMarkHMM	bed	/depot/data2/galaxy/microbes/12521/NC_008263.GeneMarkHMM.bed
+#DATA	12521_NC_008263_Glimmer3	12521	NC_008263	Glimmer3	bed	/depot/data2/galaxy/microbes/12521/NC_008263.Glimmer3.bed