details: http://www.bx.psu.edu/hg/galaxy/rev/ebc1c19fc2d5 changeset: 2875:ebc1c19fc2d5 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Mon Oct 12 16:14:54 2009 -0400 description: Changed Bowtie so that if alignment parameters cannot be read, it errors out 1 file(s) affected in this change: tools/sr_mapping/bowtie_wrapper.py diffs (14 lines): diff -r 7fd7bbe91838 -r ebc1c19fc2d5 tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Mon Oct 12 14:40:01 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Mon Oct 12 16:14:54 2009 -0400 @@ -132,8 +132,8 @@ ('','-o %s'%options.offrate)[int(options.offrate)>=0], ('','--seed %s'%options.seed)[int(options.seed)>=0], options.threads) - except ValueError: - aligning_cmds = '-p %s -S' % options.threads + except ValueError, erf: + stop_err('Something is wrong with the alignment parameters and the alignment could not be run\n' + str(erf)) # prepare actual aligning commands if options.paired == 'paired':