[2] | 1 | #This is a sample file distributed with Galaxy that enables tools |
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| 2 | #to use a directory of BFAST indexed sequences data files. You will need |
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| 3 | #to create these data files and then create a bfast_indices.loc file |
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| 4 | #similar to this one (store it in this directory) that points to |
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| 5 | #the directories in which those files are stored. The bfast_indexes.loc |
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| 6 | #file has this format (white space characters are TAB characters): |
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| 7 | # |
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| 8 | #<unique_id> <build> <galaxy format extensions valid1,valid2> <description> <bfast_index_directory> |
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| 9 | # |
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| 10 | # |
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| 11 | #So, for example, if you had hg18 indexed for 40+ bp NT reads stored in |
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| 12 | #/galaxy/data/hg18/bfast_index/nt/40+, |
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| 13 | #then the bfast_indices.loc entry could look like this: |
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| 14 | # |
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| 15 | #hg18_nt_40+ hg18 fastqsanger hg18: 40+ bp NT Space reads /galaxy/data/hg18/bfast_index/nt/40+/hg18.fa |
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| 16 | # |
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| 17 | #and your /depot/data2/galaxy/hg18/bfast/nt/40+ directory |
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| 18 | #would contain hg18.fa.*.brg and hg18.fa.*.bif files: |
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| 19 | #hg18.fa.nt.brg |
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| 20 | #hg18.fa.nt.1.1.bif |
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| 21 | #hg18.fa.nt.2.1.bif |
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| 22 | #...etc... |
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| 23 | #or similarly for color space indexes: |
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| 24 | #hg18.fa.nt.brg #NB: the localalign process requires the nucleotide brg file |
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| 25 | #hg18.fa.cs.brg |
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| 26 | #hg18.fa.cs.1.1.bif |
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| 27 | #hg18.fa.cs.2.1.bif |
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| 28 | #...etc... |
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| 29 | # |
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| 30 | #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: |
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| 31 | #hg18_standard hg18 fastqsanger,fastqcssanger hg18 standard indexes /galaxy/data/hg18/bfast_index/hg18.fa |
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| 32 | # |
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| 33 | #The use of symlinks to prevent copying of e.g. .fa and .brg files is recommended |
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| 34 | # |
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| 35 | #hg18_nt_40+ hg18 fastqsanger hg18: 40+ bp NT Space reads /galaxy/data/hg18/bfast_index/nt/40+/hg18.fa |
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| 36 | #hg18_cs_50+ hg18 fastqcssanger hg18: 50+ bp Color space reads /galaxy/data/hg18/bfast_index/cs/50+/hg18.fa |
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| 37 | #hg18_nt_40- hg18 fastqsanger hg18: 40- bp NT Space reads /galaxy/data/hg18/bfast_index/nt/40-/hg18.fa |
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| 38 | #phiX_nt_50 phiX fastqsanger phiX: 50 bp NT Space reads /galaxy/data/phiX/bfast_index/nt/50/phiX.fa |
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