[2] | 1 | #This is a sample file distributed with Galaxy that enables tools |
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| 2 | #to use alignment data stored as axt files (lines starting with "align") |
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| 3 | #or nib files (lines starting with "seq"). You will need to index |
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| 4 | #them and then create an alignseq.loc file similar to this one (store |
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| 5 | #it in this directory) that points to the directories in which those |
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| 6 | #alignments are stored. The "align" data referred to by the alignseq.loc |
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| 7 | #file has this format (white space characters are TAB characters): |
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| 8 | # |
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| 9 | #align <build1> <build2> <dir> |
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| 10 | # |
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| 11 | #So, for example, if you had hg18/bosTau2 alignment files stored in |
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| 12 | #/depot/data2/galaxy/hg18/align/bosTau2, then the alignseq.loc entry |
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| 13 | #would look like this: |
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| 14 | # |
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| 15 | #align hg18 bosTau2 /depot/data2/galaxy/hg18/align/bosTau2 |
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| 16 | # |
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| 17 | #and your /depot/data2/galaxy/hg18/align/bosTau2 directory would |
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| 18 | #contain all of your alignment files (e.g.): |
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| 19 | # |
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| 20 | #-rw-rw-r-- 1 nate galaxy 151842783 2006-01-08 01:00 chr10.axt |
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| 21 | #-rw-rw-r-- 1 nate galaxy 79575 2006-01-08 01:00 chr10_random.axt |
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| 22 | #-rw-rw-r-- 1 nate galaxy 155015634 2006-01-08 01:01 chr11.axt |
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| 23 | #...etc... |
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| 24 | # |
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| 25 | #Your alignseq.loc file should include an entry per line for each alignment |
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| 26 | #file you have stored. For example: |
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| 27 | # |
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| 28 | #align anoGam1 dm1 /depot/data2/galaxy/anoGam1/align/dm1 |
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| 29 | #align anoGam1 dm2 /depot/data2/galaxy/anoGam1/align/dm2 |
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| 30 | #align canFam1 hg17 /depot/data2/galaxy/canFam1/align/hg17 |
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| 31 | #...etc... |
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| 32 | # |
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| 33 | #The "seq" data referred to by the alignseq.loc file has this |
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| 34 | #format (white space characters are TAB characters): |
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| 35 | # |
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| 36 | #seq <build1> <dir> |
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| 37 | # |
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| 38 | #So, for example, if you had anoGam1 sequence files stored in |
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| 39 | #/depot/data2/galaxy/anoGam1/seq, then the alignseq.loc entry |
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| 40 | #would look like this: |
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| 41 | # |
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| 42 | #seq anoGam1 /depot/data2/galaxy/anoGam1/seq |
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| 43 | #and your seq anoGam1 /depot/data2/galaxy/anoGam1/seq directory would |
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| 44 | #contain all of your sequence files (e.g.): |
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| 45 | # |
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| 46 | #-rw-rw-r-- 1 nate galaxy 24397551 2006-06-26 12:51 chr2L.nib |
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| 47 | #-rw-rw-r-- 1 nate galaxy 31362964 2006-06-26 12:51 chr2R.nib |
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| 48 | #-rw-rw-r-- 1 nate galaxy 20642013 2006-06-26 12:51 chr3L.nib |
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| 49 | #-rw-rw-r-- 1 nate galaxy 26636071 2006-06-26 12:51 chr3R.nib |
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| 50 | # |
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| 51 | #Your alignseq.loc file should include an entry per line for each sequence |
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| 52 | #file you have stored. For example: |
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| 53 | # |
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| 54 | #seq anoGam1 /depot/data2/galaxy/anoGam1/seq |
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| 55 | #seq bosTau2 /depot/data2/galaxy/bosTau2/seq |
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| 56 | #seq bosTau3 /depot/data2/galaxy/bosTau3/seq |
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| 57 | #...etc... |
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