diff README_STARV2 @ 6:b7ed4ee33fb6 draft default tip

Deleted selected files

--- a/README_STARV2	Tue Dec 12 10:16:23 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-************************************************************************************
-******        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/
-
-
-