Hi

run.sh

On 05/24/2017 10:51 AM, Georgios Nikolis wrote:
Hi Hans-Rudolf,
many thanks for pointing me to the right direction. samtools was
installed, it was indeed a problem with $PATH.
There are actually path setting scripts provides with the tools, also
for samtools, e.g.
database/dependencies/samtools/0.1.19/devteam/package_samtools_0_1_19/95d2c4aefb5f/env.sh
but it seems that they don't get executed automatically on server start.
I did it manually and bwa-mem runs now without errors.
We will have to see whether other tools besides samtools are affected.
Would you recommend that we put such path setting scripts into run.sh?

yes, at least for samtools, I guess this is currently the best option.

Regards, Hans-Rudolf


Best,
Georgios

On 05/22/2017 08:11 AM, Hans-Rudolf Hotz wrote:
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 <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

logo <http://www.dkfz.de>

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





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