Hi Nicola, interesting you fixed bowtie in the same way than we did. But somehow I would like to strip a trailing ';' by default in Galaxy, when it does not break anything else.
Thanks for sharing! Bjoern > Il giorno ven, 11/10/2013 alle 01.10 +0200, Björn Grüning ha scritto: > > 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. > > The Bowtie2 bug may be fixed if my pull request 234 will be merged: > > https://bitbucket.org/galaxy/galaxy-central/pull-request/234/bug-fixes-for-3-tools-rebased-222 > > > 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? > > That would be sensible too. > > Ciao, > Nicola > ___________________________________________________________ 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/
