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