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README_STARV2 |
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| 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 |
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| @@ -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/ + + + |