Re: [galaxy-dev] cluster access

2017-05-22 Thread Matthias Bernt 

Dear list,

I had some time to dig into this.

Since this is a quite old thread here is a wrap up:

The problem was that galaxy uses the USER part of the email address 
(USER@DOMAIN) to determine the system user to submit jobs to a drmaa 
cluster (I need to submit jobs as real user). In my setting, where users 
login via LDAP, this does not work since the prefix of the email is not 
always the user name, but the actual user is stored in the galaxy data 
base (and awaited utilization :) ).


I found a way to let galaxy try both possibilities, and whatever of the 
two possibilities matches a real user is taken (prioritizing the email 
method for compatibility). I have created a pull request:


https://github.com/galaxyproject/galaxy/pull/4096

Cheers,
Matthias


On 10.04.2017 17:03, Peter Cock wrote:

That's interesting. I didn't set this up on our system, but if the LDAP can
tell Galaxy the real username, maybe we can avoid having to setup
usern...@example.org aliases and insisting our users do that for
logging into Galaxy.

Hopefully some other SGE users can comment on how they got the
run-as-user system working for them?

Peter

On Mon, Apr 10, 2017 at 3:43 PM, Matthias Bernt  wrote:

Hi,

sorry, I forgot this central piece of information: We also use Univa Grid
Engine.

What would be easier adapting galaxy's mapping to users or setting up email
aliases? I would need to ask our cluster admins if they could realize this.

Best,
Matthias



On 10.04.2017 16:39, Peter Cock wrote:


This may depend on the cluster setup, and how Galaxy accesses it.
What are you using?

We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup
usern...@example.org email aliases just for this.

Peter

On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt  wrote:


Dear list,

I'm just starting to get jobs submitted to our cluster as real system
user.
I read in the documentation that the name of the system user is
determined
by "the Galaxy user's email address (with the @domain stripped off)". But
this does not work on our system, rather the username stored in the
galaxy_user table is the name of the user (this is correctly generated by
the LDAP login).

The job runner script seems to get the user id, so I guess I need to dig
deeper. So my question is: Where could I change this behavior?

Thanks a lot.

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

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Registergericht/Registration Office: Amtsgericht Leipzig
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Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
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Wilfried Kraus
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Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
---


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--

---
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.

Re: [galaxy-dev] python subprocess OSError when running bwa-mem

2017-05-22 Thread Hans-Rudolf Hotz 

Hi Georgios

I am just guessing here, but the error looks familiar:

Do you have samtools installed? and is it in $PATH?
(for a similar case, see: https://biostar.usegalaxy.org/p/19938/ )


Regards, Hans-Rudolf


On 05/19/2017 10:03 AM, Georgios Nikolis wrote:

Dear all,
we are currently working on a new local Galaxy instance (17.01) and we
encounter an error when running bwa-mem jobs. The jobs fail with a
python subprocess OSError triggered in the module
lib/galaxy/datatypes/binary.py
Here is the traceback:

Traceback (most recent call last):
   File "/opt/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 624, in 
finish_job
 job_state.job_wrapper.finish( stdout, stderr, exit_code )
   File "/opt/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1350, in finish
 dataset.datatype.set_meta( dataset, overwrite=False )
   File "/opt/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 391, in 
set_meta
 exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' 
))
   File "/usr/lib64/python2.7/subprocess.py", line 524, in call
 return Popen(*popenargs, **kwargs).wait()
   File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
 errread, errwrite)
   File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child
 raise child_exception
OSError: [Errno 2] No such file or directory

Has anyone seen this error before? Is there anything we can do to get
rid of it?

Thanks a lot!

Best,
Georgios


--
*Georgios Nikolis*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659

g.niko...@dkfz.de 
www.dkfz.de 

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





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