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author sarahinraauzeville
date Fri, 12 Feb 2016 08:30:58 -0500
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- Complete the PATH.ini file
- To know your path to tophat2 bin, you could use this command line : 
which tophat2

- Create a "workspace" directory in /database/files/  
- chmod 777 /path/to/database/files/workspace/
- In sm_tophat2.pl file, complete the path to PATH.ini file
my $cfg = Config::IniFiles->new( -file => "/path/to/PATH.ini" );

- In your tool_conf.xml file, add this line in your RNAseq section :
 <tool file="/path/to/sm_tophat2.xml" />