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 <[email protected]> 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
