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

[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
>
> **
> The information contained in the EMail and any attachments is confidential
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> It may not be disclosed to any other person without the express authority of
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Re: [galaxy-dev] The state of the MOTHUR merge?

[Peter van Heusden]

Thanks Björn, no rush!

Is anyone here doing 16S on Galaxy? I've been looking into options, and
FastQC, Trimmomatic, PEAR and the MOTHUR tools seem to give a viable
workflow. Other options are QIIME or integrating the UPARSE pipeline as I
understand. Any comments appreciated!

Thanks,
Peter

On 3 June 2016 at 15:53, Björn Grüning  wrote:

> Me finishing my re review and pressing the merge button.
> I tend to merge as it is at the moment and do some small adjustments
> afterwards ... This weekend Peter, this weekend! :)
>
> Am 03.06.2016 um 13:37 schrieb Peter van Heusden:
> > PR #429 on tools-iuc contains the updated MOTHUR toolsuite for Galaxy.
> >
> > https://github.com/galaxyproject/tools-iuc/pull/429
> >
> > It *looks* like it is ready to merge - what is still needed before it
> > merges into tools-iuc?
> >
> > Thanks!
> > Peter
> >
> >
> > ___
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> >
>
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Re: [galaxy-dev] setting metadata externally failed for HistoryDatasetAssociation

[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
> **
>
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[galaxy-dev] setting metadata externally failed for HistoryDatasetAssociation

[Anthony Underwood]

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
**
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Re: [galaxy-dev] LDAP authentication

[mark fernandes (IFR)]

Don't know if this helps or not but here's the link to Novell's entry on LDAP 
support for eDirectory
https://www.novell.com/documentation/edir873/?page=/documentation/edir873/edir873/data/h007.html

Mark Fernandes  


T: +44 (0)1603 255000
Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK

www.ifr.ac.uk
Facebook | Twitter | LinkedIn | YouTube

The Institute of Food Research receives strategic funding from BBSRC

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Re: [galaxy-dev] The state of the MOTHUR merge?

[Björn Grüning]

Me finishing my re review and pressing the merge button.
I tend to merge as it is at the moment and do some small adjustments
afterwards ... This weekend Peter, this weekend! :)

Am 03.06.2016 um 13:37 schrieb Peter van Heusden:
> PR #429 on tools-iuc contains the updated MOTHUR toolsuite for Galaxy.
> 
> https://github.com/galaxyproject/tools-iuc/pull/429
> 
> It *looks* like it is ready to merge - what is still needed before it
> merges into tools-iuc?
> 
> Thanks!
> Peter
> 
> 
> ___
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> 
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>   http://galaxyproject.org/search/mailinglists/
> 
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[galaxy-dev] The state of the MOTHUR merge?

[Peter van Heusden]

PR #429 on tools-iuc contains the updated MOTHUR toolsuite for Galaxy.

https://github.com/galaxyproject/tools-iuc/pull/429

It *looks* like it is ready to merge - what is still needed before it
merges into tools-iuc?

Thanks!
Peter
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