/tool-data/bwa_index.loc.sample
https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 38 lines · 38 code · 0 blank · 0 comment · 0 complexity · 5b5e34001be54ae293fcea6eb9562a0b MD5 · raw file
- #This is a sample file distributed with Galaxy that enables tools
- #to use a directory of BWA indexed sequences data files. You will need
- #to create these data files and then create a bwa_index.loc file
- #similar to this one (store it in this directory) that points to
- #the directories in which those files are stored. The bwa_index.loc
- #file has this format (longer white space characters are TAB characters):
- #
- #<unique_build_id> <dbkey> <display_name> <file_path>
- #
- #So, for example, if you had phiX indexed stored in
- #/depot/data2/galaxy/phiX/base/,
- #then the bwa_index.loc entry would look like this:
- #
- #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
- #
- #and your /depot/data2/galaxy/phiX/base/ directory
- #would contain phiX.fa.* files:
- #
- #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
- #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
- #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
- #...etc...
- #
- #Your bwa_index.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:
- #
- #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
- #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
- #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
- #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
- #...etc...
- #
- #Note that for backwards compatibility with workflows, the unique ID of
- #an entry must be the path that was in the original loc file, because that
- #is the value stored in the workflow for that parameter. That is why the
- #hg19 entry above looks odd. New genomes can be better-looking.
- #