Local galaxy samtools HISAT 2 issue

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Local galaxy samtools HISAT 2 issue

evan clark
I am setting up a production galaxy server and am having an issue with running HISAT 2. It appears that it is not able to find samtools and renders an error within galaxy. Below is the error that it produces. I am unsure how to get the full error log for HISAT.

Traceback (most recent call last):
  File "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py", line 609, in finish_job
    job_state.job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", line 1265, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/home/eclark28/galaxy_production/galaxy/lib/galaxy/datatypes/binary.py", line 347, in set_meta
    exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )
  File "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 523, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 1343, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory


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Re: Local galaxy samtools HISAT 2 issue

John Chilton-4
I think this is caused because Galaxy needs to have samtools available
on its PATH. Is this an older version of Galaxy? I feel like newer
versions maybe make this error more clear.

Hope this helps - hopefully very quickly here we solve this problem by
switching to pysam for these operations so an external dependency
(poorly documented) isn't required.

-John

On Wed, Oct 12, 2016 at 12:37 PM, evan clark <[hidden email]> wrote:

> I am setting up a production galaxy server and am having an issue with
> running HISAT 2. It appears that it is not able to find samtools and renders
> an error within galaxy. Below is the error that it produces. I am unsure how
> to get the full error log for HISAT.
>
> Traceback (most recent call last):
>   File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py",
> line 609, in finish_job
>     job_state.job_wrapper.finish( stdout, stderr, exit_code )
>   File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", line
> 1265, in finish
>     dataset.datatype.set_meta( dataset, overwrite=False )
>   File
> "/home/eclark28/galaxy_production/galaxy/lib/galaxy/datatypes/binary.py",
> line 347, in set_meta
>     exit_code = subprocess.call( args=command, stderr=open( stderr_name,
> 'wb' ) )
>   File
> "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line
> 523, in call
>     return Popen(*popenargs, **kwargs).wait()
>   File
> "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line
> 711, in __init__
>     errread, errwrite)
>   File
> "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line
> 1343, in _execute_child
>     raise child_exception
> OSError: [Errno 2] No such file or directory
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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