On Nov 7, 2013, at 2:45 PM, Jean-Francois Payotte wrote:
> Dear Galaxy developers,
> I know I am not the only one with this issue, as over time I've stumbled on a
> few mailing-list threads with other users having the same problem.
> And I know the recommended solution is to use the -noac mount option.
> However, it is said that using this -noac mount option comes with a
> performance trade-off, so when we first ran into this issue (datasets showing
> "Empty" and "No peek", even though the file on the hard drive is full of
> content), we implemented the hack found in this thread:
> In this thread, John suggested to add a "sleep()" in the "finish_job" method
> of the "galaxy_dist/lib/galaxy/jobs/runnersdrmaa.py" file.
> It worked very well for us. Adding a sleep(30) made all the jobs waiting 30
> seconds before finishing, but the "No peek" issue had at least disappear).
> However, since the latest Galaxy updates, this file (drmaa.py) has been
> dramastically changed and the "finish_job" method doesn't exist anymore.
> Hence, I had to remove this hack, hoping that this issue would have
> disappeared as well. Unfortunaley, this "No peek" issue is still there and
> causing many headaches to some of our workflows users.
> My question is then: Can I put this "sleep(30)" in some other place (method
> and/or file) in order to achieve the same result?
> I would really like to solve this "No peek" issue without resorting to the
> "-noac" mount option. Actually, I am not even sure our system administrator
> would allow it.
The job runners have been largely refactored into
lib/galaxy/jobs/runners/__init__.py, which is where you'll find finish_job().
However, we also recently added some tricks to work around this issue that has
solved the problem (for usegalaxy.org, at least) without needing -noac. This
is available in Monday's distribution release. Here's the commit:
To use, set retry_job_output_collection > 0 in the Galaxy config.
> Thanks again for your help!
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