I think newer versions of Galaxy give a better error message - I am
pretty sure the problem is you are missing samtools. It needs to be
available on the PATH for Galaxy if you use bam data.

-John

On Fri, Jun 3, 2016 at 1:00 PM, Anthony Underwood
<anthony.underw...@phe.gov.uk> wrote:
>
>
> Jobs that I run on a local Galaxy install on a Fedora 23 machine are
> completing but are erroring with the message below. Any idea why the
> metadata can not be written?
>
> Thanks
>
> galaxy.jobs.runners.local DEBUG 2016-06-03 17:30:02,044 execution finished:
> /home/anthony.underwood/galaxy/database/jobs_directory/000/142/galaxy_142.sh
>     galaxy.model.metadata DEBUG 2016-06-03 17:30:02,158 setting metadata
> externally failed for HistoryDatasetAssociation 158: [Errno 2] No such file
> or directory
>     galaxy.jobs.runners.local ERROR 2016-06-03 17:30:02,235 Job wrapper
> finish method failed
>     Traceback (most recent call last):
>       File
> "/home/anthony.underwood/galaxy/lib/galaxy/jobs/runners/local.py", line 128,
> in queue_job
>         job_wrapper.finish( stdout, stderr, exit_code )
>       File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/__init__.py",
> line 1257, in finish
>         dataset.datatype.set_meta( dataset, overwrite=False )
>       File "/home/anthony.underwood/galaxy/lib/galaxy/datatypes/binary.py",
> line 339, in set_meta
>         exit_code = subprocess.call( args=command, stderr=open( stderr_name,
> 'wb' ) )
>       File "/usr/lib64/python2.7/subprocess.py", line 522, in call
>         return Popen(*popenargs, **kwargs).wait()
>       File "/usr/lib64/python2.7/subprocess.py", line 710, in __init__
>         errread, errwrite)
>       File "/usr/lib64/python2.7/subprocess.py", line 1335, in
> _execute_child
>         raise child_exception
>     OSError: [Errno 2] No such file or directory
>
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