# HG changeset patch
# User sarahinraauzeville
# Date 1513091760 18000
# Node ID aeebcdb9b8b266ed5498931ecac25f1baa294a95
# Parent  80e19490ec6a9bda1b411af31969ea4a2c16351f
Uploaded

diff -r 80e19490ec6a -r aeebcdb9b8b2 README_STARV2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README_STARV2	Tue Dec 12 10:16:00 2017 -0500
@@ -0,0 +1,82 @@
+************************************************************************************
+******        Add perl and xml wrapper files in tools/ d                      ******
+************************************************************************************
+
+Download files with hg clone in tools/ directory, then you have these files availables (wrappers and scripts):
+sm_STAR2_V2.pl  sm_STAR2_V2.xml
+GalaxyPath.pm
+STAR_indexes.loc.sample
+STAR_indexes.loc.sample
+
+Add GalaxyPath.pm file in /path/to/galaxy_sources/ directory
+
+************************************************************************************
+******       loc file                                                         ******
+************************************************************************************
+
+mv STAR_indexes.loc.sample STAR_indexes.loc
+then
+Add STAR_indexes.loc in yout tool-data/ repository 
+
+************************************************************************************
+******        tool_conf.xml file to update                                    ******
+************************************************************************************
+
+Add a tag <tool> in your section "RNAseq" (for instance) in your config/tool_conf.xml file:
+        <tool file="/path/to/sm_STAR2_V2.xml" />
+
+************************************************************************************
+******        job_conf.xml file to update                                     ******
+************************************************************************************
+Add a new section in config/job_conf.xml file, in <destinations> tag, add these lines:
+        
+        <destination id="sm_star_single_V2_job" runner="drmaa">
+		    <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
+		    <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
+		    <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
+		    <param id="nativeSpecification">-clear -V -q galaxy.q -l mem=12G -l h_vmem=16G -pe parallel_smp 2</param>
+		    <env file="/galaxydata/galaxy-prod/my_config/local_env.sh"/>
+		</destination>
+		
+and in <tools> tag:
+        	<tool id="sm_star_single_V2" destination="sm_star_single_V2_job"/>
+
+************************************************************************************
+******        tool_data_table_conf.xml file to update                         ******
+************************************************************************************
+
+Add these lines in your tool_data_table_conf.xml file:
+
+ <!-- location of loc file for STAR V2 tool -->
+    <table name="STAR_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="my_tool-data/STAR_indexes.loc" />
+    </table>
+
+************************************************************************************
+******        Add paths in galaxy.ini configuation file                       ******
+************************************************************************************
+
+Add a my_bin/ directory in galaxy repository with symbolic links to binaries:
+$ ls -ltrah /path/to/galaxy/my_bin/STAR*
+lrwxrwxrwx 1 galaxy-prod wbioinfo 11  3 juin   2016 /galaxydata/galaxy-prod/my_bin/STAR -> STAR_2.4.0i
+
+
+Add paths to binaries and a section [workPath], at the end of galaxy.ini file: 
+Dans geany ../../config/galaxy.ini &
+[workPath]
+STAR_PATH=/path/to/galaxy/my_bin/STAR
+
+
+Add a my_workspace/ directory in galaxy repository to run this module in debug mode:
+cd /path/to/galaxy/;
+mkdir my_workspace/;
+chmod 777 my_workspace/;
+
+Add paths to binaries and a section [workPath], at the end of galaxy.ini file: 
+Dans geany ../../config/galaxy.ini &
+[workPath]
+MYWORKSPACE=/path/to/galaxy/my_workspace/
+
+
+