Opps, sent that last e-mail before I meant to, gmail is acting very buggy for me this morning. I just meant to say I would modify build_command_line in lib/galaxy/jobs/runners/__init__.py instead. It seems like there is a lot of logic in there for this kind of thing already. I will create a Trello card and you.
Also just say Nate's response, he is probably right so ignore this e-mail as well :). -John On Fri, Oct 11, 2013 at 7:57 AM, John Chilton <chil0...@umn.edu> wrote: > This sounds like a good way to solve the problem, I guess I would modify > > > On Thu, Oct 10, 2013 at 6:10 PM, Björn Grüning > <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote: >> >> Dear all, >> >> some SGE instances will add automatically an semicolon add the end of >> each command, resulting in a disrupted job, because ';;' are not >> allowed. >> >> The latest changes to the Bowtie2 wrapper resulting in such a case and a >> crash in our instance. An easy solution would be to fix the wrapper and >> omitting the trailing ';' but maybe its better to fix it once for all in >> the corresponding tools code, patched attached. >> >> I'm not familiar with other Job schedulers so I'm seeking for >> comments ... it there any disadvantage of removing trailing ';' from the >> command line? >> >> Ciao, >> Bjoern >> >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/