On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote: > Hello, > > Question for galaxy maintainers: have you encountered situations where BWA > jobs run 'forever' (for days) ? > > A little digging shows that it's the "bwa sampe" step, and SEQanswers thread > mention it's somewhat common: > http://seqanswers.com/forums/showthread.php?t=11652 > http://seqanswers.com/forums/showthread.php?t=6340 > > One suggested work-around is to add "-A" to "bwa sampe", but there's no way > to do it in the current BWA wrapper. > (On the command-line with the same input files it does make things much > faster). > > I'm wondering if this is common enough to justify adding "-A" to the wrapper, > or is it rare enough and can be ignored. > > -gordon
Can it be added as an optional argument? So that if it is selected, the setting is passed to the tool, otherwise not. chris ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
