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

[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 Poznań Supercomputing and
Networking Center. Since I have become a sort of partial maintainer of it
over the years, I had long wanted to properly import the SVN repository
from PSNC and clean up my fork in GitHub to make it easier for people to
use and preserve the development history.

Your email finally compelled me to get around to it, and you should see
that https://github.com/natefoo/slurm-drmaa is in a friendlier state now.
Most notably, the default (master) branch is now the updated version of
slurm-drmaa, and I have posted a 1.2.0 development pre-release tarball
under the releases section, meaning that it's no longer necessary to
install/run the GNU autotools to generate the configure script or a source
tarball for the new as-yet-unreleased version.

I have recently been in touch with the current maintainer at PSNC, and he
is still planning to make a new release, so I am not going to make an
"official" release at this time (it's not my project, after all), but I
have tried to make it easier to use my fork in the meantime.

Thanks,
--nate

On Wed, Jun 28, 2017 at 10:57 AM, Nicola Soranzo 
wrote:

> Hi Gwen,
> thanks for reporting this issue! You are correct and similar problems have
> been reported frequently on the mailing list and on Gitter/IRC. If you go
> to https://galaxyproject.org/admin/config/performance/cluster/ and click
> on the "Edit" button, you can modify the page yourself on GitHub and open a
> pull request.
>
> That's just to say that even if the website is not a classic wiki any
> more, we encourage everybody to contribute!
>
> Thanks again!
> Nicola
>
>
>
> On 28/06/17 11:59, Dawes, Gwen wrote:
>
>> Hi folks,
>> I just had a bit of an interesting problem with Galaxy. We have a
>> configuration whereby work is submitted to our friendly local SLURM cluster
>> via DRMAA. However, the PSNC base version is too old to be able to parse
>> the more modern slurm configs, and was repeatedly failing to submit,
>> stating that it was unable to parse slurm.conf.
>>
>> The updated version of this library by natefoo (
>> https://github.com/natefoo/slurm-drmaa ) using the multicluster branch
>> works perfectly for submitting to a more modern SLURM, but this isn't
>> referenced at the Admin/Config/Cluster page on galaxyproject.org . Can
>> someone update this information?
>>
>> Thanks!
>> ___
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>>
>
> ___
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Re: [galaxy-dev] tool and planemo problems

[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/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.
>>
>> 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.
>>>
>>> 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 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
>> 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 successful, but in
>> the
>> end I still get a fail -- verbose mode is also of no help here.
>>
>> Applying linter tests... CHECK
>> .. CHECK: 7 test(s) found.
>> Applying linter output... CHECK
>> .. INFO: 1 outputs found.
>> Applying linter inputs... CHECK
>> .. INFO: Found 3 input parameters.
>> Applying linter help... CHECK
>> .. CHECK: Tool contains help section.
>> .. CHECK: Help contains valid reStructuredText.
>> Applying linter general... CHECK
>> .. CHECK: Tool defines a version [0.1.0].
>> .. CHECK: Tool defines a name [Waste time and memory].
>> .. CHECK: Tool defines an id [sleepwaste].
>> .. CHECK: Tool targets 16.01 Galaxy profile.
>> Applying linter command... CHECK
>> .. INFO: Tool contains a command.
>> Applying linter citations... WARNING
>> .. WARNING: No citations found, consider adding citations to your tool.
>> Applying linter tool_xsd... CHECK
>> .. INFO: File validates against XML schema.
>> Failed linting
>>
>> The test of the tool are all successful. Any ideas what is wrong?
>>
>> Once the problems are solved, would such a tool also be useful in the
>> toolshed?
>>
>> Cheers,
>> Matthias
>>
>>
>>
>> --
>>
>> ---
>> Matthias Bernt
>> Bioinformatics Service
>> Molekulare Systembiologie (MOLSYB)
>> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
>> Helmholtz Centre for Environmental Research GmbH - UFZ
>> Permoserstraße 15, 04318 Leipzig, Germany
>> Phone +49 341 235 482296,
>> m.be...@ufz.de, www.ufz.de
>>
>> Sitz der Gesellschaft/Registered Office: Leipzig
>> Registergericht/Registration Office: Amtsgericht Leipzig
>> Handelsregister Nr./Trade Register Nr.: B 4703
>> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
>> MinDirig
>> Wilfried Kraus
>> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
>> Prof. Dr. Dr. h.c. Georg Teutsch
>> Administrative Geschäftsführerin/ Administrative Managing Director:
>> Prof. Dr. Heike Graßmann
>> ---
>>
>> ___
>> 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:
>> https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/



 --

 ---
 Matthias Bernt
 Bioinformatics Service
 Molekulare Systembiologie (MOLSYB)
 Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
 Helmholtz Centre for Environmental Research GmbH - UFZ
 Permoserstraße 15, 04318 Leipzig, Germany
 Phone +49 341 235 482296,
 m.be...@ufz.de, www.ufz.de

 Sitz der Gesellschaft/Registered Office: Leipzig
 Registergericht/Registration Office: Amtsgericht Leipzig
 Handelsregister Nr./Trade Register Nr.: B 4703
 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
 MinDirig
 Wilfried Kraus
 Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
 Prof. Dr. Dr. h.c. Georg T

Re: [galaxy-dev] tool and planemo problems

[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.
>
> 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.
>>
>> 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 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
> 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 successful, but in
> the
> end I still get a fail -- verbose mode is also of no help here.
>
> Applying linter tests... CHECK
> .. CHECK: 7 test(s) found.
> Applying linter output... CHECK
> .. INFO: 1 outputs found.
> Applying linter inputs... CHECK
> .. INFO: Found 3 input parameters.
> Applying linter help... CHECK
> .. CHECK: Tool contains help section.
> .. CHECK: Help contains valid reStructuredText.
> Applying linter general... CHECK
> .. CHECK: Tool defines a version [0.1.0].
> .. CHECK: Tool defines a name [Waste time and memory].
> .. CHECK: Tool defines an id [sleepwaste].
> .. CHECK: Tool targets 16.01 Galaxy profile.
> Applying linter command... CHECK
> .. INFO: Tool contains a command.
> Applying linter citations... WARNING
> .. WARNING: No citations found, consider adding citations to your tool.
> Applying linter tool_xsd... CHECK
> .. INFO: File validates against XML schema.
> Failed linting
>
> The test of the tool are all successful. Any ideas what is wrong?
>
> Once the problems are solved, would such a tool also be useful in the
> toolshed?
>
> Cheers,
> Matthias
>
>
>
> --
>
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296,
> m.be...@ufz.de, www.ufz.de
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
> MinDirig
> Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> ---
>
> ___
> 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:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/
>>>
>>>
>>>
>>> --
>>>
>>> ---
>>> Matthias Bernt
>>> Bioinformatics Service
>>> Molekulare Systembiologie (MOLSYB)
>>> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
>>> Helmholtz Centre for Environmental Research GmbH - UFZ
>>> Permoserstraße 15, 04318 Leipzig, Germany
>>> Phone +49 341 235 482296,
>>> m.be...@ufz.de, www.ufz.de
>>>
>>> Sitz der Gesellschaft/Registered Office: Leipzig
>>> Registergericht/Registration Office: Amtsgericht Leipzig
>>> Handelsregister Nr./Trade Register Nr.: B 4703
>>> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
>>> MinDirig
>>> Wilfried Kraus
>>> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
>>> Prof. Dr. Dr. h.c. Georg Teutsch
>>> Administrative Geschäftsführerin/ Administrative Managing Director:
>>> Prof. Dr. Heike Graßmann
>>> ---
>
>
> --
>
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centr

Re: [galaxy-dev] tool and planemo problems

[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.

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 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
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 successful, but in
the
end I still get a fail -- verbose mode is also of no help here.

Applying linter tests... CHECK
.. CHECK: 7 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 3 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.1.0].
.. CHECK: Tool defines a name [Waste time and memory].
.. CHECK: Tool defines an id [sleepwaste].
.. CHECK: Tool targets 16.01 Galaxy profile.
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... WARNING
.. WARNING: No citations found, consider adding citations to your tool.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Failed linting

The test of the tool are all successful. Any ideas what is wrong?

Once the problems are solved, would such a tool also be useful in the
toolshed?

Cheers,
Matthias



--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig
Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---

___
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:
https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/



--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig
Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---


--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
MinDirig Wilfried Kraus

Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
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 int

Re: [galaxy-dev] tool and planemo problems

[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 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
>>> 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 successful, but in
>>> the
>>> end I still get a fail -- verbose mode is also of no help here.
>>>
>>> Applying linter tests... CHECK
>>> .. CHECK: 7 test(s) found.
>>> Applying linter output... CHECK
>>> .. INFO: 1 outputs found.
>>> Applying linter inputs... CHECK
>>> .. INFO: Found 3 input parameters.
>>> Applying linter help... CHECK
>>> .. CHECK: Tool contains help section.
>>> .. CHECK: Help contains valid reStructuredText.
>>> Applying linter general... CHECK
>>> .. CHECK: Tool defines a version [0.1.0].
>>> .. CHECK: Tool defines a name [Waste time and memory].
>>> .. CHECK: Tool defines an id [sleepwaste].
>>> .. CHECK: Tool targets 16.01 Galaxy profile.
>>> Applying linter command... CHECK
>>> .. INFO: Tool contains a command.
>>> Applying linter citations... WARNING
>>> .. WARNING: No citations found, consider adding citations to your tool.
>>> Applying linter tool_xsd... CHECK
>>> .. INFO: File validates against XML schema.
>>> Failed linting
>>>
>>> The test of the tool are all successful. Any ideas what is wrong?
>>>
>>> Once the problems are solved, would such a tool also be useful in the
>>> toolshed?
>>>
>>> Cheers,
>>> Matthias
>>>
>>>
>>>
>>> --
>>>
>>> ---
>>> Matthias Bernt
>>> Bioinformatics Service
>>> Molekulare Systembiologie (MOLSYB)
>>> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
>>> Helmholtz Centre for Environmental Research GmbH - UFZ
>>> Permoserstraße 15, 04318 Leipzig, Germany
>>> Phone +49 341 235 482296,
>>> m.be...@ufz.de, www.ufz.de
>>>
>>> Sitz der Gesellschaft/Registered Office: Leipzig
>>> Registergericht/Registration Office: Amtsgericht Leipzig
>>> Handelsregister Nr./Trade Register Nr.: B 4703
>>> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
>>> MinDirig
>>> Wilfried Kraus
>>> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
>>> Prof. Dr. Dr. h.c. Georg Teutsch
>>> Administrative Geschäftsführerin/ Administrative Managing Director:
>>> Prof. Dr. Heike Graßmann
>>> ---
>>>
>>> ___
>>> 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:
>>>https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>http://galaxyproject.org/search/
>
>
> --
>
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296,
> m.be...@ufz.de, www.ufz.de
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig
> Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> ---
___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

Re: [galaxy-dev] tool and planemo problems

[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 Bernt  wrote:

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 successful, but in the
end I still get a fail -- verbose mode is also of no help here.

Applying linter tests... CHECK
.. CHECK: 7 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 3 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.1.0].
.. CHECK: Tool defines a name [Waste time and memory].
.. CHECK: Tool defines an id [sleepwaste].
.. CHECK: Tool targets 16.01 Galaxy profile.
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... WARNING
.. WARNING: No citations found, consider adding citations to your tool.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Failed linting

The test of the tool are all successful. Any ideas what is wrong?

Once the problems are solved, would such a tool also be useful in the
toolshed?

Cheers,
Matthias



--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig
Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---

___
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:
   https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/


--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
MinDirig Wilfried Kraus

Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] tool and planemo problems

[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
> 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 successful, but in the
> end I still get a fail -- verbose mode is also of no help here.
>
> Applying linter tests... CHECK
> .. CHECK: 7 test(s) found.
> Applying linter output... CHECK
> .. INFO: 1 outputs found.
> Applying linter inputs... CHECK
> .. INFO: Found 3 input parameters.
> Applying linter help... CHECK
> .. CHECK: Tool contains help section.
> .. CHECK: Help contains valid reStructuredText.
> Applying linter general... CHECK
> .. CHECK: Tool defines a version [0.1.0].
> .. CHECK: Tool defines a name [Waste time and memory].
> .. CHECK: Tool defines an id [sleepwaste].
> .. CHECK: Tool targets 16.01 Galaxy profile.
> Applying linter command... CHECK
> .. INFO: Tool contains a command.
> Applying linter citations... WARNING
> .. WARNING: No citations found, consider adding citations to your tool.
> Applying linter tool_xsd... CHECK
> .. INFO: File validates against XML schema.
> Failed linting
>
> The test of the tool are all successful. Any ideas what is wrong?
>
> Once the problems are solved, would such a tool also be useful in the
> toolshed?
>
> Cheers,
> Matthias
>
>
>
> --
>
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296,
> m.be...@ufz.de, www.ufz.de
>
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
> Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig
> Wilfried Kraus
> Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> ---
>
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[galaxy-dev] tool and planemo problems

[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 successful, but in 
the end I still get a fail -- verbose mode is also of no help here.


Applying linter tests... CHECK
.. CHECK: 7 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 3 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.1.0].
.. CHECK: Tool defines a name [Waste time and memory].
.. CHECK: Tool defines an id [sleepwaste].
.. CHECK: Tool targets 16.01 Galaxy profile.
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... WARNING
.. WARNING: No citations found, consider adding citations to your tool.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Failed linting

The test of the tool are all successful. Any ideas what is wrong?

Once the problems are solved, would such a tool also be useful in the 
toolshed?


Cheers,
Matthias



--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
MinDirig Wilfried Kraus

Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---


sleepwaste.tar.bz2
Description: application/bzip
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[galaxy-dev] Issues with "bamtools split", running jobs don't show up in history (and fail after several hours)

[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":

"tool error

An error occurred with this dataset:
Unable to finish job"

All versions (Galaxy, bamtools 2.4.0,samtools 1.3.1) are up to date and
this is what I installed:

Repositorybamtools_split
Name:  bamtools_split
Owner: devteam
Synopsis:  Tool for splitting BAM files
Detailed description: Utility for splitting BAM files. It is based on
BAMtools suite of tools by Derek Barnett.
Content homepage:  https://github.com/pezmaster31/bamtools

Development repository:
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split

Revision: 2:e2c1b62e1db1

Thanks and best regards,

Christopher


-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

christopher.prev...@dkfz.de 
www.dkfz.de 

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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