Hi Anthony,

The line numbers for binary.py don't match the current
latest source, but I would bet this is due to the samtools
binary not being on the path of the cluster nodes. Note
Galaxy itself needs samtools for dealing with BAM files
and this is expected to be on the $PATH (and it not
currently handled via the Galaxy Tool dependency
system).

Peter

On Fri, Jun 3, 2016 at 6:00 PM, Anthony Underwood
<Anthony.Underwood@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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