Hey All, Patch available with test case, let me know what I broke :).
https://bitbucket.org/jmchilton/galaxy-central-multi-input-tool-fixes-2/commits/e0016057e1648d7f4d29fbaf14252cbefff6d0bd -John On Fri, Oct 11, 2013 at 10:37 AM, Björn Grüning <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote: > Am Freitag, den 11.10.2013, 09:18 -0500 schrieb John Chilton: >> My plan is to refactor build_command_line out of >> lib/galaxy/jobs/runners/__init__.py, into its own module and add unit >> tests for this functionality. I'll issue a pull request and let people >> test it. I am also testing Nicola's PR, I will approve it shortly. >> >> Nate yelled at me for committing code yesterday :) so I will let him >> figure out when to merge it. But I will approve the pull requests that >> I am willing to say are tested and that I will take responsibility for >> if something breaks in them. > > Ok, sounds good! > > Thanks! > Bjoern > >> -John >> >> On Fri, Oct 11, 2013 at 9:13 AM, Björn Grüning >> <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote: >> > Ah now I got it ... there are two build_command_line functions. >> > lib/galaxy/tools/__init__.py and lib/galaxy/jobs/runners/__init__.py. >> > >> > And one is adding a trailing ';' >> > >> > So either stripping the trailing semicolon, right after creating the >> > command line from cheetah (patch was attached) or adding more logic to >> > only add a ';' when no one is there. >> > >> > Which one is preferred, should I create a pull request? >> > >> > Thanks! >> > Bjoern >> > >> > >> >> If the tool produces a trailing semi-colon (and without Nicola's patch >> >> the bowtie 2 tool definitely could), then I bet build_command_line() >> >> is going to be what is adding the second semi-colon. It has not check >> >> that there isn't a semi-colon at the end of the command before adding >> >> one and extending the command. It might not be the only culprit, but >> >> it is likely one. >> >> >> >> -John >> >> >> >> On Fri, Oct 11, 2013 at 9:02 AM, Björn Grüning >> >> <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote: >> >> > Hi Nate, >> >> > >> >> >> Hi Björn, >> >> >> >> >> >> Are you certain that SGE is responsible? I ran in to the same thing >> >> >> with bowtie2 with other runners. >> >> >> The double semicolon is invalid syntax in Bourne-compatible shells and >> >> >> so the tool ought to be fixed not to produce them (it happens under >> >> >> certain combinations of options). >> >> >> Have you noticed this happening with any other tools? >> >> > >> >> > Yes, but only with tools from the toolshed and there I poked people to >> >> > remove the trailing semicolon from the wrapper. From my observation the >> >> > tool does not produce double semicolons. Only one at the end, but the >> >> > Job scheduler adds one, resulting in a double one with invalid syntax. >> >> > >> >> > I can't see where bowtie is producing a double semicolon. I really think >> >> > SGE is adding one. At least I restructured the semicolons (attached) and >> >> > it worked for us. >> >> > >> >> > Thanks Nate, >> >> > Bjoern >> >> > >> >> >> --nate >> >> >> >> >> >> On Oct 11, 2013, at 8:57 AM, John Chilton 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. 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