diff tool-data/muse_index.loc.sample @ 3:b3152fc222fb draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/muse_index.loc.sample	Thu Oct 18 08:17:26 2018 -0400
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+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of MuSE  fasta files. You will need
+#to create these data files and then create a muse_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The muse_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.dict, phiX.fa.fai files.
+#
+#
+#Your mutect2_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	GRCh38.d1.vd1.fa	/cvmfs/elixir-italy.galaxy.refdata/GRCh38.d1.vd1/GRCh38.d1.vd1.fa
+hg38	hg38	hg38_GATK_bundle	/cvmfs/elixir-italy.galaxy.refdata/index_GATK_bundle/Homo_sapiens_assembly38/Homo_sapiens_assembly38.fasta
+hg19	hg19	hg19_GATK_bundle	/cvmfs/elixir-italy.galaxy.refdata/index_GATK_bundle/ucsc.hg19/ucsc.hg19.fasta
+