I think this is caused because Galaxy needs to have samtools available on its PATH. Is this an older version of Galaxy? I feel like newer versions maybe make this error more clear. Hope this helps - hopefully very quickly here we solve this problem by switching to pysam for these operations so an external dependency (poorly documented) isn't required. -John On Wed, Oct 12, 2016 at 12:37 PM, evan clark <eclark28@fau.edu> wrote:
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 such file or directory
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/