Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
Martin Cech
@martenson
someone please merge galaxyproject/galaxy#5685
galaxybot
@galaxybot
[mrscribe] Title: [18.01] add security announcement to the release notes by martenson · Pull Request #5685 · galaxyproject/galaxy · GitHub (at github.com)
Dannon
@dannon
Is galaxyproject/galaxy#5572 something we need to get into 18.01?
galaxybot
@galaxybot
[mrscribe] Title: Fix/default role type on auto created roles by scholtalbers · Pull Request #5572 · galaxyproject/galaxy · GitHub (at github.com)
Dannon
@dannon
(there's cruft from the retargeting, looks like, but the fix itself is what I'm referring to)
Qiang Gu
@qiagu
galaxyproject/galaxy#5687
Galaxy uWSGI process got Segmentation Fault on OS X. This problem happens occasionally in my MAC. I feel it's a problem of uWSGI, not Galaxy. Maybe an upgrade of uWSGI could solve the problem.
Nicola Soranzo
@nsoranzo
@natefoo ^
Nate Coraor
@natefoo
@qiagu: can you try ./.venv/bin/pip uninstall -y uwsgi && ./.venv/bin/pip install --no-cache-dir --no-binary :all: -y uwsgi?
Qiang Gu
@qiagu
The uninstallation worked, but the installation didn't.
error: no such file or directory: '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.a'
error linking uWSGI
Nate Coraor
@natefoo
that's strange
Qiang Gu
@qiagu
Also, 'no option -y' for the installation part. The message was produced by removing the '-y'.
Dannon
@dannon
D'oh. Was just replying to the github issue you made.
Nate Coraor
@natefoo
oh right, pip install doesn't have a prompt
Dannon
@dannon
After we tracked down the issue I was having with the uwsgi wheel you built a new one, right?
Nate Coraor
@natefoo
yeah i think?
Dannon
@dannon
Yeah, I thought so too, was just trying to track through all we did to fix it.
:q
...
Ok, so mine was __CF_USER_TEXT_ENCODING being set or not causing the segfault.
(when unset, reliably segfaulted -- when set everything was peachy)
Nate Coraor
@natefoo
yeah but that was a red herring.
here's the fix i ultimately applied: unbit/uwsgi#1680
galaxybot
@galaxybot
[mrscribe] Title: Reinitialize environ after uwsgi_setup_reload() when running as a CPython extension on macOS by natefoo · Pull Request #1680 · unbit/uwsgi · GitHub (at github.com)
Dannon
@dannon
Hrmm. Not a peep on the PR on their end, kind of a bummer.
Nate Coraor
@natefoo
yeah. =(
and unfortunately the wheel should already be fixed.
Martin Cech
@martenson
There hasn’t been any commit activity on unbit/uwsgi in the last week.
Dannon
@dannon
Well, the fourth frame there is different, mine coming through libxpc and this new one thorugh libobjc.A
Not sure if that's a clue, may take some more digging though.
Qiang Gu
@qiagu
Oh, I remember the problem only occurs when the galaxy.yml is applied.
Martin Cech
@martenson
@qiagu that just implies uwsgi, .ini would always use Paste I think
Alexander Lenail
@zfrenchee
Should a download from a data library automatically cut off after 1GB?
Martin Cech
@martenson
@zfrenchee No.
Alexander Lenail
@zfrenchee
@martenson if all downloads seem to persistently cut off after 1GB, where should I look?
Martin Cech
@martenson
anything in the server logs?
James Taylor
@jxtx
What's the \sigma ?
Martin Cech
@martenson
@jxtx sum
Nate Coraor
@natefoo
\Sigma ;)
Jessica
@tue60565
Hey, my name is Jessica. I think the job queue for usegalaxy, which I believe is hosted at TACC, has a large backlog. Is there anything that can be done?
galaxybot
@galaxybot
[jxtx] Still don't understand the summation.
Martin Cech
@martenson
it is not math, just emoji, 'the sum of 469 pull requests'
Sorry if it is unclear/confusing.
Alexander Lenail
@zfrenchee
@martenson thanks for answering. Bjoern and I resolved it =)
Jennifer Hillman-Jackson
@jennaj
@tue60565 Hi Jessica, the job queue was very busy earlier today but it looks as if jobs are moving again. The server was likely just busy but out admin @natefoo will comment more if needed.
For now, allow queued jobs to stay queued until they execute. More details are in this Q&A from earlier today https://biostar.usegalaxy.org/p/27109/
galaxybot
@galaxybot
[mrscribe] Title: This job is waiting to run at Galaxy Main https://usegalaxy.org - Larger clusters are busy, please leave jobs queued until they execute (at biostar.usegalaxy.org)
Rajeev Vikram
@darkrid_twitter
Hi, I am trying to sun a set of jobs since yesterday on galaxy main, but nothings moving
*run and not sun
And when I try to log out, I get a "Failed to authorize Action" Msg