Mercurial > repos > sarahinraauzeville > star
comparison README_STARV2 @ 6:b7ed4ee33fb6 draft default tip
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| author | sarahinraauzeville |
|---|---|
| date | Mon, 09 Dec 2019 10:55:33 -0500 |
| parents | c4fc8ff6e280 |
| children |
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| 5:c4fc8ff6e280 | 6:b7ed4ee33fb6 |
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| 1 ************************************************************************************ | |
| 2 ****** Add perl and xml wrapper files in tools/ d ****** | |
| 3 ************************************************************************************ | |
| 4 | |
| 5 Download files with hg clone in tools/ directory, then you have these files availables (wrappers and scripts): | |
| 6 sm_STAR2_V2.pl sm_STAR2_V2.xml | |
| 7 GalaxyPath.pm | |
| 8 STAR_indexes.loc.sample | |
| 9 STAR_indexes.loc.sample | |
| 10 | |
| 11 Add GalaxyPath.pm file in /path/to/galaxy_sources/ directory | |
| 12 | |
| 13 ************************************************************************************ | |
| 14 ****** loc file ****** | |
| 15 ************************************************************************************ | |
| 16 | |
| 17 mv STAR_indexes.loc.sample STAR_indexes.loc | |
| 18 then | |
| 19 Add STAR_indexes.loc in yout tool-data/ repository | |
| 20 | |
| 21 ************************************************************************************ | |
| 22 ****** tool_conf.xml file to update ****** | |
| 23 ************************************************************************************ | |
| 24 | |
| 25 Add a tag <tool> in your section "RNAseq" (for instance) in your config/tool_conf.xml file: | |
| 26 <tool file="/path/to/sm_STAR2_V2.xml" /> | |
| 27 | |
| 28 ************************************************************************************ | |
| 29 ****** job_conf.xml file to update ****** | |
| 30 ************************************************************************************ | |
| 31 Add a new section in config/job_conf.xml file, in <destinations> tag, add these lines: | |
| 32 | |
| 33 <destination id="sm_star_single_V2_job" runner="drmaa"> | |
| 34 <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> | |
| 35 <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> | |
| 36 <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> | |
| 37 <param id="nativeSpecification">-clear -V -q galaxy.q -l mem=12G -l h_vmem=16G -pe parallel_smp 2</param> | |
| 38 <env file="/galaxydata/galaxy-prod/my_config/local_env.sh"/> | |
| 39 </destination> | |
| 40 | |
| 41 and in <tools> tag: | |
| 42 <tool id="sm_star_single_V2" destination="sm_star_single_V2_job"/> | |
| 43 | |
| 44 ************************************************************************************ | |
| 45 ****** tool_data_table_conf.xml file to update ****** | |
| 46 ************************************************************************************ | |
| 47 | |
| 48 Add these lines in your tool_data_table_conf.xml file: | |
| 49 | |
| 50 <!-- location of loc file for STAR V2 tool --> | |
| 51 <table name="STAR_indexes" comment_char="#"> | |
| 52 <columns>value, dbkey, name, path</columns> | |
| 53 <file path="my_tool-data/STAR_indexes.loc" /> | |
| 54 </table> | |
| 55 | |
| 56 ************************************************************************************ | |
| 57 ****** Add paths in galaxy.ini configuation file ****** | |
| 58 ************************************************************************************ | |
| 59 | |
| 60 Add a my_bin/ directory in galaxy repository with symbolic links to binaries: | |
| 61 $ ls -ltrah /path/to/galaxy/my_bin/STAR* | |
| 62 lrwxrwxrwx 1 galaxy-prod wbioinfo 11 3 juin 2016 /galaxydata/galaxy-prod/my_bin/STAR -> STAR_2.4.0i | |
| 63 | |
| 64 | |
| 65 Add paths to binaries and a section [workPath], at the end of galaxy.ini file: | |
| 66 Dans geany ../../config/galaxy.ini & | |
| 67 [workPath] | |
| 68 STAR_PATH=/path/to/galaxy/my_bin/STAR | |
| 69 | |
| 70 | |
| 71 Add a my_workspace/ directory in galaxy repository to run this module in debug mode: | |
| 72 cd /path/to/galaxy/; | |
| 73 mkdir my_workspace/; | |
| 74 chmod 777 my_workspace/; | |
| 75 | |
| 76 Add paths to binaries and a section [workPath], at the end of galaxy.ini file: | |
| 77 Dans geany ../../config/galaxy.ini & | |
| 78 [workPath] | |
| 79 MYWORKSPACE=/path/to/galaxy/my_workspace/ | |
| 80 | |
| 81 | |
| 82 |