1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/94bfcccdaf06/ changeset: 94bfcccdaf06 user: jgoecks date: 2013-01-08 15:25:16 summary: Fix bug in bowtie2 wrapper that prevented wrapper from working with old versions of samtools. affected #: 1 file diff -r 989c789fbc43b0d9960655752c6ba396ac7618af -r 94bfcccdaf0625448e623d1d88ba9a1b7785ee78 tools/sr_mapping/bowtie2_wrapper.py --- a/tools/sr_mapping/bowtie2_wrapper.py +++ b/tools/sr_mapping/bowtie2_wrapper.py @@ -71,7 +71,7 @@ index_path = options.index_path # Build bowtie command; use view and sort to create sorted bam. - cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - sorted > %s' + cmd = 'bowtie2 %s -x %s %s | samtools view -Su - | samtools sort -o - - > %s' # Set up reads. if options.single_paired == 'paired': 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.