Thanks Peter and John - this was exactly the issue- problem solved. Not very intuitive but an easy fix :) On 3 June 2016 at 23:13:34, Peter Cock (p.j.a.cock@googlemail.com<mailto:p.j.a.cock@googlemail.com>) wrote: 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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