Mercurial > repos > jjohnson > shear
comparison tool-data/bwa_index.loc.sample @ 0:65255beda972
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| author | jjohnson |
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| date | Fri, 08 Nov 2013 16:23:10 -0500 |
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| -1:000000000000 | 0:65255beda972 |
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| 1 #This is a sample file distributed with Galaxy that enables tools | |
| 2 #to use a directory of BWA indexed sequences data files. You will need | |
| 3 #to create these data files and then create a bwa_index.loc file | |
| 4 #similar to this one (store it in this directory) that points to | |
| 5 #the directories in which those files are stored. The bwa_index.loc | |
| 6 #file has this format (longer white space characters are TAB characters): | |
| 7 # | |
| 8 #<unique_build_id> <dbkey> <display_name> <file_path> | |
| 9 # | |
| 10 #So, for example, if you had phiX indexed stored in | |
| 11 #/depot/data2/galaxy/phiX/base/, | |
| 12 #then the bwa_index.loc entry would look like this: | |
| 13 # | |
| 14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa | |
| 15 # | |
| 16 #and your /depot/data2/galaxy/phiX/base/ directory | |
| 17 #would contain phiX.fa.* files: | |
| 18 # | |
| 19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb | |
| 20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann | |
| 21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt | |
| 22 #...etc... | |
| 23 # | |
| 24 #Your bwa_index.loc file should include an entry per line for each | |
| 25 #index set you have stored. The "file" in the path does not actually | |
| 26 #exist, but it is the prefix for the actual index files. For example: | |
| 27 # | |
| 28 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa | |
| 29 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa | |
| 30 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa | |
| 31 #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa | |
| 32 #...etc... | |
| 33 # | |
| 34 #Note that for backwards compatibility with workflows, the unique ID of | |
| 35 #an entry must be the path that was in the original loc file, because that | |
| 36 #is the value stored in the workflow for that parameter. That is why the | |
| 37 #hg19 entry above looks odd. New genomes can be better-looking. | |
| 38 # |