Moderator: Nate Coraor

gravatar for Nate Coraor
Nate Coraor3.2k
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Joined:
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Email:
n***@bx.psu.edu

Posts by Nate Coraor

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Comment: C: sge drmaa cluster galaxy configuration
... Ok, at this stage I think it would be best to continue this on IRC, or the galaxy-dev mailing list if I miss your question on IRC. ...
written 10 weeks ago by Nate Coraor3.2k
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Comment: C: sge drmaa cluster galaxy configuration
... Sorry I missed your reply. If you're still having issues, please let me know. This heartbeat log appears to show the threads in an idle state. To run the daemon handler, you can install daemonize in the virtualenv with `./.venv/bin/pip install daemonize`. ...
written 12 weeks ago by Nate Coraor3.2k
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Comment: C: sge drmaa cluster galaxy configuration
... I would suggest running a separate ["webless" handler](https://docs.galaxyproject.org/en/master/admin/scaling.html#uwsgi-webless-job-handling) so that you can isolate the heartbeat to that process. ...
written 3 months ago by Nate Coraor3.2k
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Comment: C: sge drmaa cluster galaxy configuration
... After the native specification message you should see more, e.g.: ``` galaxy.jobs.runners.drmaa DEBUG 2018-05-03 08:48:34,950 (19306430) native specification is: --partition=normal --nodes=1 --ntasks=1 --time=36:00:00 galaxy.jobs.runners.drmaa INFO 2018-05-03 08:48:34,964 (19306430) queued as 134 ...
written 3 months ago by Nate Coraor3.2k
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Answer: A: sge drmaa cluster galaxy configuration
... The pbs directory isn't used any more, the job script is written directly to the job's working directory is the only copy. The Galaxy job handler's logs should indicate if there was an error submitting to SGE. ...
written 3 months ago by Nate Coraor3.2k
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Answer: A: uWSGI mule setup + nginx fails
... uWSGI should create the socket. However, there's a mistake in the docs. The value of uWSGI's `socket` option is not a URL, so it should look like this: ``` uwsgi: socket: /opt/galaxy/var/uwsgi.sock ``` I'll submit a correction for the docs - sorry for the inconvenience. As to why you're not a ...
written 3 months ago by Nate Coraor3.2k
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Comment: C: Tool errors with private instance of Galaxy on Jetstream
... The Jetstream image does attempt to mirror the same tools as usegalaxy.org but beyond that it's very different from usegalaxy.org in the way it is configured and tools are installed. This situation looks pretty ugly. Part of the issue stems from the fact that Galaxy in Jetstream is currently versio ...
written 4 months ago by Nate Coraor3.2k
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Comment: C: Adding Custom Build is failing
... Sorry, I missed your reply. Have you gotten this working? If not, can you explain a bit about how your Galaxy server is set up? Specifically: - What version of Galaxy? - Are you using a proxy server, and if so, which one, and how is it configured to proxy requests to Galaxy? - Are you using uWSGI o ...
written 4 months ago by Nate Coraor3.2k
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Comment: A: Tool errors with private instance of Galaxy on Jetstream
... Is there additional context to the error message? This almost looks like a corrupt conda installation, although there is something else strange here, which is that Galaxy is creating a per-job Conda environment when you run the tool. That should only happen if your tools' dependencies are not "mulle ...
written 5 months ago by Nate Coraor3.2k
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Comment: C: MPileup SNP and indel caller (Galalxy Version 0.0.1) error
... I'm looking in to whether this can be fixed. In general we make a strong commitment to keep things that once worked, working forever after. But this is not always possible to do, especially for tools that predate the more robust dependency management that we've added over the past few years. ...
written 5 months ago by Nate Coraor3.2k

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