Mercurial > repos > sarahinraauzeville > rnaseq_tophat2

comparison README_tophat2_toolshed @ 6:60f0a4bd7f97 draft default tip

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author sarahinraauzeville
date Fri, 12 Feb 2016 08:30:58 -0500
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5:04b86e142e90 6:60f0a4bd7f97
1 - Complete the PATH.ini file
2 - To know your path to tophat2 bin, you could use this command line :
3 which tophat2
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5 - Create a "workspace" directory in /database/files/
6 - chmod 777 /path/to/database/files/workspace/
7 - In sm_tophat2.pl file, complete the path to PATH.ini file
8 my $cfg = Config::IniFiles->new( -file => "/path/to/PATH.ini" );
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10 - In your tool_conf.xml file, add this line in your RNAseq section :
11 <tool file="/path/to/sm_tophat2.xml" />
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