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Greg Von Kuster
58 lines
2.3 KiB
Plaintext
58 lines
2.3 KiB
Plaintext
#This is a sample file distributed with Galaxy that enables tools
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#to use alignment data stored as axt files (lines starting with "align")
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#or nib files (lines starting with "seq"). You will need to index
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#them and then create an alignseq.loc file similar to this one (store
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#it in this directory) that points to the directories in which those
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#alignments are stored. The "align" data referred to by the alignseq.loc
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#file has this format (white space characters are TAB characters):
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#
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#align <build1> <build2> <dir>
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#
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#So, for example, if you had hg18/bosTau2 alignment files stored in
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#/depot/data2/galaxy/hg18/align/bosTau2, then the alignseq.loc entry
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#would look like this:
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#
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#align hg18 bosTau2 /depot/data2/galaxy/hg18/align/bosTau2
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#
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#and your /depot/data2/galaxy/hg18/align/bosTau2 directory would
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#contain all of your alignment files (e.g.):
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#
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#-rw-rw-r-- 1 nate galaxy 151842783 2006-01-08 01:00 chr10.axt
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#-rw-rw-r-- 1 nate galaxy 79575 2006-01-08 01:00 chr10_random.axt
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#-rw-rw-r-- 1 nate galaxy 155015634 2006-01-08 01:01 chr11.axt
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#...etc...
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#
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#Your alignseq.loc file should include an entry per line for each alignment
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#file you have stored. For example:
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#
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#align anoGam1 dm1 /depot/data2/galaxy/anoGam1/align/dm1
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#align anoGam1 dm2 /depot/data2/galaxy/anoGam1/align/dm2
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#align canFam1 hg17 /depot/data2/galaxy/canFam1/align/hg17
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#...etc...
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#
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#The "seq" data referred to by the alignseq.loc file has this
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#format (white space characters are TAB characters):
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#
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#seq <build1> <dir>
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#
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#So, for example, if you had anoGam1 sequence files stored in
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#/depot/data2/galaxy/anoGam1/seq, then the alignseq.loc entry
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#would look like this:
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#
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#seq anoGam1 /depot/data2/galaxy/anoGam1/seq
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#and your seq anoGam1 /depot/data2/galaxy/anoGam1/seq directory would
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#contain all of your sequence files (e.g.):
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#
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#-rw-rw-r-- 1 nate galaxy 24397551 2006-06-26 12:51 chr2L.nib
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#-rw-rw-r-- 1 nate galaxy 31362964 2006-06-26 12:51 chr2R.nib
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#-rw-rw-r-- 1 nate galaxy 20642013 2006-06-26 12:51 chr3L.nib
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#-rw-rw-r-- 1 nate galaxy 26636071 2006-06-26 12:51 chr3R.nib
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#
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#Your alignseq.loc file should include an entry per line for each sequence
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#file you have stored. For example:
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#
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#seq anoGam1 /depot/data2/galaxy/anoGam1/seq
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#seq bosTau2 /depot/data2/galaxy/bosTau2/seq
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#seq bosTau3 /depot/data2/galaxy/bosTau3/seq
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#...etc...
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