view README_STARV2 @ 3:aeebcdb9b8b2 draft

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******        Add perl and xml wrapper files in tools/ d                      ******
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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

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******       loc file                                                         ******
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mv STAR_indexes.loc.sample STAR_indexes.loc
then
Add STAR_indexes.loc in yout tool-data/ repository 

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******        tool_conf.xml file to update                                    ******
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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" />

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******        job_conf.xml file to update                                     ******
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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"/>

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******        tool_data_table_conf.xml file to update                         ******
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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>

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******        Add paths in galaxy.ini configuation file                       ******
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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/