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.
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.
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
>> 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
>>> 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
>>> errread, errwrite)
>>> File "/usr/lib64/python2.7/subprocess.py", line 1327, in
>>> 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!
>> *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
>> phone: +49 6221 42-4659
>> g.nikolis(a)dkfz.de <http://www.dkfz.de/>
>> logo <http://www.dkfz.de>
>> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
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