Mercurial > repos > ieguinoa > data_manager_salmon_index_builder

changeset 9:9004217cddf4 draft default tip

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Uploaded
author ieguinoa
date Tue, 23 Jul 2019 12:18:12 -0400
parents cbe62bd6e149
children
files data_manager_conf.xml tool-data/all_fasta.loc.sample
diffstat 2 files changed, 2 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager_conf.xml	Tue Jul 23 11:12:15 2019 -0400
+++ b/data_manager_conf.xml	Tue Jul 23 12:18:12 2019 -0400
@@ -9,9 +9,9 @@
                 <column name="path" output_ref="out_file" >
                     <move type="directory" relativize_symlinks="True">
                         <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/salmon_index/${value}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/salmon_index/${value}/${version}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/salmon_index/${value}/${path}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/salmon_index/${value}/${version}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
                 <column name="version" />
--- a/tool-data/all_fasta.loc.sample	Tue Jul 23 11:12:15 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-#This file lists the locations and dbkeys of all the fasta files
-#under the "genome" directory (a directory that contains a directory
-#for each build). The script extract_fasta.py will generate the file
-#all_fasta.loc. This file has the format (white space characters are
-#TAB characters):
-#
-#<unique_build_id>	<dbkey>	<display_name>	<file_path>
-#
-#So, all_fasta.loc could look something like this:
-#
-#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
-#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
-#
-#Your all_fasta.loc file should contain an entry for each individual
-#fasta file. So there will be multiple fasta files for each build,
-#such as with hg19 above.
-#