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README_tophat2_toolshed |
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| diff -r f50a064ebd1c -r b89fa46df3a7 README_tophat2_toolshed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_tophat2_toolshed Thu Feb 11 08:45:52 2016 -0500 |
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| @@ -0,0 +1,18 @@ +- Create a PATH.ini file in galaxy-dist/ repository: +- Add these 3 lines in your PATH.ini file : +TOPHAT2_PATH=/path/to/bin/tophat2 +FILEPATH_DEV=/path/to/database/files/workspace/ +BOWTIE2_INDEXATION_PATH=/path/to/bin/bowtie2 + +- 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" /> + + |