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 suchfile or directory|