# HG changeset patch
# User elixir-it
# Date 1569086475 14400
# Node ID 110b3018eb2ac7895099133e7ac9f0a1f35eeda4
# Parent  b48eb134cfcc2b36c2c51c4d6c196719c6735873
Uploaded

diff -r b48eb134cfcc -r 110b3018eb2a tool-data/gatk_sorted_picard_index.loc.sample
--- a/tool-data/gatk_sorted_picard_index.loc.sample	Fri Sep 20 08:25:16 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +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.
-#
-#hg19	hg19	hg19_GATK_bundle	/cvmfs/elixir-italy.galaxy.refdata/index_GATK_bundle/ucsc.hg19/ucsc.hg19.fasta
-
diff -r b48eb134cfcc -r 110b3018eb2a tool-data/muse_index.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/muse_index.loc.sample	Sat Sep 21 13:21:15 2019 -0400
@@ -0,0 +1,34 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of MuSE indexed sequences data 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 muse_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.
+#
diff -r b48eb134cfcc -r 110b3018eb2a tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Fri Sep 20 08:25:16 2019 -0400
+++ b/tool_data_table_conf.xml.sample	Sat Sep 21 13:21:15 2019 -0400
@@ -2,6 +2,6 @@
     <!-- Locations of indexes in the muse_call mapper format -->
     <table name="muse_index" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-        <file path="/cvmfs/data.galaxyproject.org/byhand/location/gatk_sorted_picard_index.loc" />
+        <file path="tool-data/muse_index.loc" />
     </table>
 </tables>