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3
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1 - Create a PATH.ini file in galaxy-dist/ repository:
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2 - Add these 3 lines in your PATH.ini file :
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3 TOPHAT2_PATH=/path/to/bin/tophat2
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4 FILEPATH_DEV=/path/to/database/files/workspace/
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5 BOWTIE2_INDEXATION_PATH=/path/to/bin/bowtie2
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6
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7 - To know your path to tophat2 bin, you could use this command line :
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8 which tophat2
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9
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10 - Create a "workspace" directory in /database/files/
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11 - chmod 777 /path/to/database/files/workspace/
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12 - In sm_tophat2.pl file, complete the path to PATH.ini file
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13 my $cfg = Config::IniFiles->new( -file => "/path/to/PATH.ini" );
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14
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15 - In your tool_conf.xml file, add this line in your RNAseq section :
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16 <tool file="/path/to/sm_tophat2.xml" />
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17
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18
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