1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a7049f42a9d9/ changeset: a7049f42a9d9 user: jgoecks date: 2013-01-09 19:36:33 summary: Add parameter to Tophat2 so that output BAM is ordered using reference contigs ordering rather than sorted lexicographically. affected #: 1 file diff -r 184c5e409425da36556de7edda910a7ffe6bc9d0 -r a7049f42a9d9b4bef6804dee53a2bc8bcc1a2916 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -134,7 +134,7 @@ index_path = options.index_path # Build tophat command. - cmd = 'tophat2 %s %s %s' + cmd = 'tophat2 --keep-fasta-order %s %s %s' reads = options.input1 if options.input2: reads += ' ' + options.input2 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.