Hey Nikos,

Thanks for the interest in the LWR and frankly I am excited to hear
that bowtie worked properly. Some of these core NGS tools that require
implicit indices spanning multiple files are not really addressed by
the LWR currently, it only knows how to stage files that actually
appear in the command-line or a config file. I guess if you are just
using files from the history this is not a problem, but it is
something to be aware of if you plan to start using .loc files.

My first thought is that the LWR might not support 'from_work_dir'
outputs in nested subdirectories. I will have to look more closely at
that. Something that will help me though, is knowing if TopHat
produced the outputs.

Can you look at the LWR staging directory and tell me if these files
were created (by default when a job fails, it is not cleaned up this
is configurable in galaxy-central but not in galaxy-dist right now)?
Also, does the LWR have any useful logs available? These will likely
be in paster.log in the LWR directory.

Also, the tip of galaxy-central includes improved error logging and
exception handling so it is possible it would produce a better error
message than this admittedly cryptic problem. I know it is not always
possible to upgrade, but if it is easy it is something worth
considering doing.

-John

On Tue, Jun 18, 2013 at 8:18 AM, Nikos Sidiropoulos
<nikos.sidiro@gmail.com> wrote:
> 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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