Re: [galaxy-dev] Issue with SLURM-DRMAA

2017-07-12 Thread Nate Coraor
Hi Gwen, I'm not the canonical source for slurm-drmaa, although development on the original version has slowed and there haven't been any releases since the death of the previous principal maintainer at the PoznaƄ Supercomputing and Networking Center. Since I have become a sort of partial maintain

Re: [galaxy-dev] tool and planemo problems

2017-07-12 Thread Peter Cock
And mere minutes later that change has been accepted, and will be part of the next release of Planemo. Thanks for the constructive feedback Matthias! Peter On Wed, Jul 12, 2017 at 4:24 PM, Peter Cock wrote: > Good idea, pull request submitted: > > https://github.com/galaxyproject/planemo/pull/7

Re: [galaxy-dev] tool and planemo problems

2017-07-12 Thread Peter Cock
Good idea, pull request submitted: https://github.com/galaxyproject/planemo/pull/709 Peter On Wed, Jul 12, 2017 at 4:03 PM, Matthias Bernt wrote: > Perfect. Thanks a lot. Maybe one could add a note to planemo --help that > command specific help can be obtained with planemo command --help. > > B

Re: [galaxy-dev] tool and planemo problems

2017-07-12 Thread Matthias Bernt
Perfect. Thanks a lot. Maybe one could add a note to planemo --help that command specific help can be obtained with planemo command --help. Best, Matthias On 12.07.2017 16:57, Peter Cock wrote: Try: planemo lint --fail_level error sleepwaste.xml The default is to fail if there are warnings.

Re: [galaxy-dev] tool and planemo problems

2017-07-12 Thread Peter Cock
Try: planemo lint --fail_level error sleepwaste.xml The default is to fail if there are warnings. Peter On Wed, Jul 12, 2017 at 3:55 PM, Matthias Bernt wrote: > Hi Peter, > > I just call planemo l sleepwaste.xml > > Best, > Matthias > > > On 12.07.2017 16:54, Peter Cock wrote: >> >> How are y

Re: [galaxy-dev] tool and planemo problems

2017-07-12 Thread Matthias Bernt
Hi Peter, I just call planemo l sleepwaste.xml Best, Matthias On 12.07.2017 16:54, Peter Cock wrote: How are you running planemo lint - in particular is it set to fail if there are any warnings present (like your missing citation warning)? Peter On Wed, Jul 12, 2017 at 3:52 PM, Matthias Bern

Re: [galaxy-dev] tool and planemo problems

2017-07-12 Thread Peter Cock
How are you running planemo lint - in particular is it set to fail if there are any warnings present (like your missing citation warning)? Peter On Wed, Jul 12, 2017 at 3:52 PM, Matthias Bernt wrote: > Dear list, > > In order to test the job resubmission feature I wrote a little tool for > galax

[galaxy-dev] tool and planemo problems

2017-07-12 Thread Matthias Bernt
Dear list, In order to test the job resubmission feature I wrote a little tool for galaxy that just wastes a specified (minimum) time and memory (using different programming languages) for testing the new DRMAA job runner that I wrote. When linting it with planemo seemingly all tests are suc

[galaxy-dev] Issues with "bamtools split", running jobs don't show up in history (and fail after several hours)

2017-07-12 Thread Previti
Dear all, I've been trying to properly install the "BAMTools split" tool in our local DKFZ-Galaxy instance, but it doesn't work properly. The strange thing is that you can launch a bamtools splitter job on our cluster, but it never shows up in the history...until it fails with following "error":