I attempted to run a job using HISAT2 on galaxy and in the console it shows samtools not found, however the job finishes with a completed bam file. The issue is that galaxy marks the job with an error as unable to finish, even though it did successfully. Do I need to install samtools in the galaxy share for my cluster or is there another issue I may be having? Below is the last call.
Traceback (most recent call last): File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py", line 609, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", line 1274, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/mnt/VDisk/galaxy_production/galaxy/lib/galaxy/datatypes/binary.py", line 355, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.7/subprocess.py", line 524, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory