Hi We are running the latest stable distribution on our server. We want tophat2 (along with other tools) to be executed on another machine. LWR is setup based on the online documentation ( http://wiki.galaxyproject.org/Admin/Config/LWR, https://lwr.readthedocs.org/en/latest/) Bowtie2 is working as should but it looks like LWR is unable to return the outputs from tophat2. In universe_wsgi.ini the runner is configured like this: [galaxy:tool_runners] bowtie2 = lwr://https://uniquestring@chaos:8913 tophat2 = lwr://https://uniquestring@chaos:8913 When running tophat2 the following error message is returned. Traceback (most recent call last): File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 135, in finish_job client.download_work_dir_output(source_file, job_wrapper.working_directory, output_file) File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py", line 146, in download_work_dir_output self.__raw_download_output(name, self.job_id, "work_dir", output) File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py", line 174, in __raw_download_output output_path=output_path) File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py", line 52, in __raw_execute response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py", line 21, in execute response = self._url_open(request, data) File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py", line 12, in _url_open return urllib2.urlopen(request, data) File "/usr/lib/python2.7/urllib2.py", line 127, in urlopen return _opener.open(url, data, timeout) File "/usr/lib/python2.7/urllib2.py", line 407, in open response = meth(req, response) File "/usr/lib/python2.7/urllib2.py", line 520, in http_response 'http', request, response, code, msg, hdrs) File "/usr/lib/python2.7/urllib2.py", line 445, in error return self._call_chain(*args) File "/usr/lib/python2.7/urllib2.py", line 379, in _call_chain result = func(*args) File "/usr/lib/python2.7/urllib2.py", line 528, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error We tried to specify tophat's output folder either directly in lwr's working or output directory without success. Is there a solution to this? Bests, Nikos