Mercurial > repos > sarahinraauzeville > rnaseq_tophat2

changeset 6:60f0a4bd7f97 draft default tip

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Uploaded
author sarahinraauzeville
date Fri, 12 Feb 2016 08:30:58 -0500
parents 04b86e142e90
children
files README_tophat2_toolshed
diffstat 1 files changed, 13 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README_tophat2_toolshed	Fri Feb 12 08:30:58 2016 -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" />  
+
+