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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. | -
| - | # | -
| - | - | -
| - | hg19_chr12 hg19_chr12 hg19_chr12 /data/refs/hg19/chr12.fa | -
| - | hg19_chr20 hg19_chr20 hg19_chr20 /data/refs/hg19/chr20.fa | -