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39 lines
1.8 KiB
Plaintext
39 lines
1.8 KiB
Plaintext
#This is a sample file distributed with Galaxy that enables tools
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#to use a directory of BWA indexed sequences data files. You will need
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#to create these data files and then create a bwa_index.loc file
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#similar to this one (store it in this directory) that points to
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#the directories in which those files are stored. The bwa_index.loc
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#file has this format (longer white space characters are TAB characters):
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#
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#<unique_build_id> <dbkey> <display_name> <file_path>
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#
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#So, for example, if you had phiX indexed stored in
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#/depot/data2/galaxy/phiX/base/,
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#then the bwa_index.loc entry would look like this:
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#
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#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
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#
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#and your /depot/data2/galaxy/phiX/base/ directory
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#would contain phiX.fa.* files:
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#
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#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
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#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
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#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
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#...etc...
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#
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#Your bwa_index.loc file should include an entry per line for each
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#index set you have stored. The "file" in the path does not actually
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#exist, but it is the prefix for the actual index files. For example:
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#
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#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
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#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
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#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
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#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
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#...etc...
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#
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#Note that for backwards compatibility with workflows, the unique ID of
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#an entry must be the path that was in the original loc file, because that
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#is the value stored in the workflow for that parameter. That is why the
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#hg19 entry above looks odd. New genomes can be better-looking.
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#
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