Mercurial > repos > sarahinraauzeville > star

comparison README_STARV2 @ 3:aeebcdb9b8b2 draft

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author sarahinraauzeville
date Tue, 12 Dec 2017 10:16:00 -0500
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2:80e19490ec6a 3:aeebcdb9b8b2
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
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82