Re: [galaxy-dev] GCC2107 Update: Oral presentation abstracts due 15 April

[Peter Cock]

Hello all,

In addition to 15 April being the GCC2017 Oral Presentation
deadline, it is also the next Open Bioinformatics Foundation
(OBF) Travel Fellowship application deadline.

The program offers up to USD $1000 and is aimed at increasing
diverse participation at events promoting open source bioinformatics
software development and open science in the biological research
community (like the Galaxy Community Conference).

http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/
https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md

Regards,

Peter

(Dr Peter Cock, OBF Treasurer)


On Thu, Apr 13, 2017 at 10:02 PM, Dave Clements
 wrote:
> Hello all,
>
>
> This is just a reminder of some GCC2017 deadlines:
>
>
>   15 April:  Oral presentation abstracts are due this Saturday at 23:59
> Paris local time.
>
>   15 May:  Early registration ends
>
>   27 May:  Poster presentation abstracts are due.
>
>   27 May:  Visualization and Computer Demo presentation abstracts are due.
>
>   31 May:  Regular registration ends
>
>   23 June: Lightning Talk presentation abstracts are due.
>
>
> About GCC2017:
>
> GCC2017 will be in Montpellier, France, 26-30 June and will feature two days
> of presentations, discussions, poster sessions, lightning talks, computer
> demos, keynotes, and birds-of-a-feather meetups, all about data-intensive
> biology and the tools that support it. GCC2017 also includes data and coding
> hackathons, and two days of training covering 16 different topics.
>
> GCC2017 will be held at Le Corum Conference Centre in the heart of
> Montpellier, just 10km from the Mediterranean. This event will gather
> several hundred researchers addressing diverse questions and facing common
> challenges in data intensive life science research. GCC participants work
> across the tree of life, come from around the world, and work at
> universities, research organizations, industry, medical schools and research
> hospitals.  If you work in or support data intensive life science research
> then GCC2017 is an ideal opportunity to present your work.
>
>
> Early registration is starts at less than 55€ / day for post-docs and
> students.  You can also book low cost conference housing when you register.
>
>
> GCC2017 has sold out all premiere sponsorship slots (a first). If you are
> interested in sponsoring (or know someone who is) there are still Silver and
> Bronze and Hackathon sponsorships available. Contact the organisers if you
> are interested.
>
>
> About Galaxy
>
> Galaxy is an open, web-based platform for data-intensive biomedical analysis
> used by tens of thousands of researchers around the world.  It supports ad
> hoc exploration and analysis through scalable and repeatable data analysis
> pipelines for large research studies. Galaxy is available in over 90 free
> and publicly accessible web servers, on commercial and national cloud
> infrastructures, and is locally installed at hundreds, if not thousands, of
> research organisations around the world.
>
>
> We hope to see you this summer in Montpellier!
>
>
> Au revoir,
>
>
> The GCC2017 Organising Committee
>
>
>
> --
> https://galaxyproject.org/
> https://getgalaxy.org/
> https://usegalaxy.org/
> https://gcc2017.sciencesconf.org/
>
> ___
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>
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[galaxy-dev] GCC2107 Update: Oral presentation abstracts due 15 April

[Dave Clements]

Hello all,


This is just a reminder of some *GCC2017
* deadlines:


  15 April:  Oral presentation abstracts
 are due* this Saturday *at 23:59
Paris local time*.*

  15 May:  Early registration
 ends

  27 May:  Poster presentation abstracts
 are due.

  27 May:  Visualization and Computer Demo presentation abstracts
 are due.

  31 May:  Regular registration
 ends

  23 June: Lightning Talk presentation abstracts
 are due.

*About GCC2017:*

GCC2017 will be in Montpellier, France, 26-30 June and will feature two
days of presentations, discussions, poster sessions, lightning talks,
computer demos, keynotes, and birds-of-a-feather meetups, all about
data-intensive biology and the tools that support it. GCC2017 also includes
data and coding hackathons ,
and two days of training 
covering 16 different topics.

GCC2017 will be held at Le Corum Conference Centre
 in the heart
of Montpellier , just 10km
from the Mediterranean. This event will gather several hundred researchers
addressing diverse questions and facing common challenges in data intensive
life science research. GCC participants work across the tree of life, come
from around the world, and work at universities, research organizations,
industry, medical schools and research hospitals.  If you work in or
support data intensive life science research then GCC2017 is an ideal
opportunity to present your work.


Early registration  is
starts at less than 55€ / day for post-docs and students.  You can also book
low cost conference housing 
when you register.


GCC2017 has sold out *all* premiere *sponsorship*
 slots (a first). If you
are interested in sponsoring (or know someone who is) there are still
Silver and Bronze and Hackathon sponsorships available. Contact the
organisers if you are interested.

About Galaxy

Galaxy  is an open, web-based platform for
data-intensive biomedical analysis used by tens of thousands of researchers
around the world.  It supports ad hoc exploration and analysis through
scalable and repeatable data analysis pipelines for large research studies.
Galaxy is available in over 90 free and publicly accessible web servers, on
commercial and national cloud infrastructures, and is locally installed at
hundreds, if not thousands, of research organisations around the world.


We hope to see you this summer in Montpellier!


Au revoir,


The GCC2017 Organising Committee


-- 
https://galaxyproject.org/
https://getgalaxy.org/
https://usegalaxy.org/
https://gcc2017.sciencesconf.org/
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Re: [galaxy-dev] drmaa on univa grid engine

[Marius van den Beek]

Hi Matthias,

in addition to the link you posted there is also this here that looks
similar:
http://dev.list.galaxyproject.org/DRMAA-options-for-SGE-td4140931.html

Perhaps qsub is filling in a default queue, and drmaa is not doing that?
You could try adding a queue to the nativeSpecification.

Good luck,
Marius

On 13 April 2017 at 15:02, Matthias Bernt  wrote:

> Dear list,
>
> I'm struggling to get jobs running on our cluster (UGE).
>
> In the galaxy log I see:
>
> galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10) submitting
> file /gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory
> /000/10/galaxy_10.sh
>
> galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10)  native
> specification is: -l h_rt=60 -l h_vmem=1G -pe smp 2
>
> and I get
>
> galaxy.jobs.runners.drmaa WARNING 2017-04-13 12:24:57,805 (10)
> drmaa.Session.runJob() failed, will retry: code 17: error: no suitable
> queues
>
> But manual submission works:
>
> qsub -l h_rt=60 -l h_vmem=1G -pe smp 2 /gpfs1/data/galaxy_server/gala
> xy-dev/database/jobs_directory/000/10/galaxy_10.sh
> Your job 161150 ("galaxy_10.sh") has been submitted
>
> So I checked if I can use the drmaa library to submit using the following
> python script (based on the example2 included in the library):
>
> """
> #!/usr/bin/env python
>
> from __future__ import print_function
> import drmaa
> import os
>
>
> def main():
> """Submit a job.
> Note, need file called sleeper.sh in current directory.
> """
> s = drmaa.Session()
> s.initialize()
> print('Creating job template')
> jt = s.createJobTemplate()
> jt.remoteCommand = os.getcwd() + '/sleeper.sh'
> jt.args = ['42','Simon says:']
> jt.joinFiles=True
> jt.nativeSpecification = "-l h_rt=60 -l h_vmem=1G -pe smp 2"
>
> jobid = s.runJob(jt)
> print('Your job has been submitted with id ' + jobid)
>
> print('Cleaning up')
> s.deleteJobTemplate(jt)
> s.exit()
>
> if __name__=='__main__':
> main()
> """
>
> This gives me the same error:
>
> drmaa.errors.DeniedByDrmException: code 17: error: no suitable queues
>
> So it seems to be a problem related to the drmaa python library.
> Unfortunately I can not try without any native specs, since time, memory
> and cores need to be specifies (a suitable queue is chosen automatically).
>
> I found an earlier post with the same error (but this seemed to be caused
> by colons in the file name): http://dev.list.galaxyproject.
> org/Galaxy-with-Univa-Grid-Engine-UGE-instead-of-SGE-tt46578
> 48.html#a4657952
>
> Does anyone has suggestions for me?
>
> Best regards,
> 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/
>
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>   http://galaxyproject.org/search/
>
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[galaxy-dev] drmaa on univa grid engine

[Matthias Bernt]

Dear list,

I'm struggling to get jobs running on our cluster (UGE).

In the galaxy log I see:

galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10) submitting 
file 
/gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory/000/10/galaxy_10.sh


galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10)  native 
specification is: -l h_rt=60 -l h_vmem=1G -pe smp 2


and I get

galaxy.jobs.runners.drmaa WARNING 2017-04-13 12:24:57,805 (10) 
drmaa.Session.runJob() failed, will retry: code 17: error: no suitable 
queues


But manual submission works:

qsub -l h_rt=60 -l h_vmem=1G -pe smp 2 
/gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory/000/10/galaxy_10.sh

Your job 161150 ("galaxy_10.sh") has been submitted

So I checked if I can use the drmaa library to submit using the 
following python script (based on the example2 included in the library):


"""
#!/usr/bin/env python

from __future__ import print_function
import drmaa
import os


def main():
"""Submit a job.
Note, need file called sleeper.sh in current directory.
"""
s = drmaa.Session()
s.initialize()
print('Creating job template')
jt = s.createJobTemplate()
jt.remoteCommand = os.getcwd() + '/sleeper.sh'
jt.args = ['42','Simon says:']
jt.joinFiles=True
jt.nativeSpecification = "-l h_rt=60 -l h_vmem=1G -pe smp 2"

jobid = s.runJob(jt)
print('Your job has been submitted with id ' + jobid)

print('Cleaning up')
s.deleteJobTemplate(jt)
s.exit()

if __name__=='__main__':
main()
"""

This gives me the same error:

drmaa.errors.DeniedByDrmException: code 17: error: no suitable queues

So it seems to be a problem related to the drmaa python library. 
Unfortunately I can not try without any native specs, since time, memory 
and cores need to be specifies (a suitable queue is chosen automatically).


I found an earlier post with the same error (but this seemed to be 
caused by colons in the file name): 
http://dev.list.galaxyproject.org/Galaxy-with-Univa-Grid-Engine-UGE-instead-of-SGE-tt4657848.html#a4657952


Does anyone has suggestions for me?

Best regards,
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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