- 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" />