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