Mercurial > repos > sarahinraauzeville > rnaseq_tophat2

comparison README_tophat2_toolshed @ 3:b89fa46df3a7 draft

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author sarahinraauzeville
date Thu, 11 Feb 2016 08:45:52 -0500
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2:f50a064ebd1c 3:b89fa46df3a7
1 - Create a PATH.ini file in galaxy-dist/ repository:
2 - Add these 3 lines in your PATH.ini file :
3 TOPHAT2_PATH=/path/to/bin/tophat2
4 FILEPATH_DEV=/path/to/database/files/workspace/
5 BOWTIE2_INDEXATION_PATH=/path/to/bin/bowtie2
6
7 - To know your path to tophat2 bin, you could use this command line :
8 which tophat2
9
10 - Create a "workspace" directory in /database/files/
11 - chmod 777 /path/to/database/files/workspace/
12 - In sm_tophat2.pl file, complete the path to PATH.ini file
13 my $cfg = Config::IniFiles->new( -file => "/path/to/PATH.ini" );
14
15 - In your tool_conf.xml file, add this line in your RNAseq section :
16 <tool file="/path/to/sm_tophat2.xml" />
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