Re: [galaxy-dev] setting metadata externally failed for HistoryDatasetAssociation

2016-06-03 Thread Peter Cock 
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
 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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Re: [galaxy-dev] setting metadata externally failed for HistoryDatasetAssociation

2016-06-03 Thread John Chilton 
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
 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
>
> **
> The information contained in the EMail and any attachments is confidential
> and intended solely and for the attention and use of the named addressee(s).
> It may not be disclosed to any other person without the express authority of
> Public Health England, or the intended recipient, or both. If you are not
> the intended recipient, you must not disclose, copy, distribute or retain
> this message or any part of it. This footnote also confirms that this EMail
> has been swept for computer viruses by Symantec.Cloud, but please re-sweep
> any attachments before opening or saving. http://www.gov.uk/PHE
> **
>
> ___
> Please keep all replies on the list by using "reply all"
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