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
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