I encountered this error message while I was trying to run RNA STAR 2.4.0 (owner:iuc, revision: ace9f5a2b40f ) on my data:
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
This error looks exactly the same as the one I posted several weeks earlier. This of course led me to believe that it could come from the same cause, that samtools can not be found by RNA Star.
I checked the tool dependency directory ( ~/galaxy-dev/tool_dependency/samtools/0.1.19/devteam/package_samtools_0_1_19/95d2c4aefb5f ) and see that there is an env.sh file. So this should be fine?
Now, adding samtools to the system PATH might not be a good idea because different tools might actually use different version of samtools.
Since I ran into the same problem with Bowtie2 and RNA Star, I tend to believe that there is a common mistake I make. Could anyone advice me on how to solve ( or troubleshoot ) this issue?