This is the problem I keep running into with both Tophat and RNA-Star on my locally installed Galaxy. They both cannot finish the job and save me the following error message:
Traceback (most recent call last): File "/home/chuonglab/galaxy-dev/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/chuonglab/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1248, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/chuonglab/galaxy-dev/lib/galaxy/datatypes/binary.py", line 339, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory
From my experience, I suspect this come from the fact that when Tophat and RNA-Star are run, the environment is not set up correctly for them so they can't find the samtools they need. Adding path to samtools binary to system PATH variable apparently might not be a good solution because different tools require different versions of samtools.
But when I monitored the process through top command, I see that tophat2 can find samtools 0.1.18 that it needs, even when I supply the path to samtools 0.1.19 system-side. It's in the last process when Galaxy is trying to finish up the task that it encounters a problem. So maybe at this point it's the samtools that's available system-wise that is needed? So probably just install a samtools package on Ubuntu should properly solve this problem? This package won't actually be used by different repository tools but only used by binary.py upon finishing a job?