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 <eclar...@fau.edu> 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
>
>
>
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