# HG changeset patch
# User sarahinraauzeville
# Date 1455198352 18000
# Node ID b89fa46df3a79d7cbe5c56abe397740c511ec0d6
# Parent  f50a064ebd1c1b0dee55afb9e8aed590efd292fb
Uploaded

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
@@ -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" />  
+
+