Mercurial > repos > mvdbeek > bam_readtagger
view bwa_mem_index.loc.sample @ 70:f383ca1c5033 draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
author | mvdbeek |
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date | Tue, 05 Nov 2019 05:06:18 -0500 |
parents | 301316cb596a |
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#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. #