view tool-data/covacs_gatk_indexes.loc.sample @ 0:c785cec34cdc draft

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#This is a sample file distributed with Galaxy that enables tools
#to use a directory of all covacs wrapper that need a gatk reference. You will need
#to create these data files and then create a covacs_gatk_indexes.loc file
#similar to this one (store it in this directory) that points to
#the directories in which those files are stored. The covacs_gatk_indexes.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.dict, phiX.fa.fai files.
#
#
#Your covacs_gatk_indexes.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.
#
hg38	hg38	hg38_GDC	/export/gatkhg38pl/GRCh38.d1.vd1.fa
hg19	hg19	hg19	/export/gatk_hg19_index_bundle/ucsc.hg19.fasta