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changeset 3:b3152fc222fb draft

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Uploaded
author elixir-it
date Thu, 18 Oct 2018 08:17:26 -0400
parents 0a8461a7b3bb
children 3112ea6b2c52
files tool-data/muse_index.loc tool-data/muse_index.loc.sample
diffstat 2 files changed, 38 insertions(+), 38 deletions(-) [+]
line wrap: on
line diff
--- a/tool-data/muse_index.loc	Thu Oct 18 08:13:27 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-#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
-
--- /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
@@ -0,0 +1,38 @@
+#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
+