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|