Hi, Bjoern,
I've tried the latest galaxy version with Torque 4.1.7, and it seems
all right. But torque version 4.2 won't work.
And I tried to submit“fastqc readqc” jobs via torque (runner pbs), but
the job is always in the queue waiting. I submited “fastqc readqc”local
All the feedbacks are welcome.
Regards
2014-07-21 19:15 GMT+02:00 Björn Grüning bjoern.gruen...@gmail.com:
Very cool, I will give it a try :)
Am 21.07.2014 16:27, schrieb Rémy Dernat:
Hi,
I created a little repository on github to parse or create wrapper files.
I
have not implemented
Hi Ben,
if the job is in waiting in the queue it's unlikely (not impossible)
that it is Galaxy fault. Can you recheck your Torque setup and how many
cores and memory your job has requested?
Ciao,
Bjoern
Am 22.07.2014 10:09, schrieb 王渭巍:
Hi, Bjoern,
I've tried the latest galaxy
On Mon, Jul 21, 2014 at 6:51 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Currently the checkout options consist of hg clones, and archives that
mercurial produces.
Having pulled or cloned galaxy a few times lately, I'm wondering if anyone
would have a use for a once-run galaxy instance in an
Hi Aaron and Eric,
Am 21.07.2014 22:58, schrieb Aaron Petkau:
Hello Eric,
That sounds like a pretty good idea. If there was a pre-built image
available for whatever release I wanted to test against I could just cache
it and (hopefully) get my tests running a bit faster. I'm not sure if
Hi Björn,
On July 22, 2014 3:17:38 AM CDT, Björn Grüning bjoern.gruen...@gmail.com
wrote:
Hi Aaron and Eric,
Am 21.07.2014 22:58, schrieb Aaron Petkau:
Hello Eric,
That sounds like a pretty good idea. If there was a pre-built image
available for whatever release I wanted to test against I
Hi Peter,
On July 22, 2014 3:15:41 AM CDT, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Jul 21, 2014 at 6:51 PM, Eric Rasche rasche.e...@yandex.ru
wrote:
Currently the checkout options consist of hg clones, and archives
that
mercurial produces.
Having pulled or cloned galaxy a few
On Tue, Jul 22, 2014 at 1:15 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Hi Peter,
On July 22, 2014 3:15:41 AM CDT, Peter Cock p.j.a.c...@googlemail.com wrote:
Given how close you can get now for minimal effort,
this seem unnecessary.
Hi Eric,
That sounds like a pretty good idea. If there was a pre-built image
available for whatever release I wanted to test against I could just
cache
it and (hopefully) get my tests running a bit faster. I'm not sure
if
anyone else is already doing this?
Also, I remember there being
Hi Björn,
22.07.2014, 14:26, Björn Grüning bjoern.gruen...@gmail.com:
Hi Eric,
That sounds like a pretty good idea. If there was a pre-built image
available for whatever release I wanted to test against I could just
cache
it and (hopefully) get my tests running a bit faster. I'm
I could use a little bit of help in making some changes to our galaxy server.
I'm in the process of setting up/testing a production galaxy server for our
research computing center. Our server is setup with an apache proxy, ldap
authentication and jobs will run as the logged in user.
The
:) great I like it!
Will do it shortly!
Am 22.07.2014 15:36, schrieb Eric Rasche:
Hi Björn,
22.07.2014, 14:26, Björn Grüning bjoern.gruen...@gmail.com:
Hi Eric,
That sounds like a pretty good idea. If there was a pre-built image
available for whatever release I wanted to test
That's awesome Björn and Eric. And, I'll also have to go through your
Travis CI document Peter. It looks really cool.
Aaron
On Tue, Jul 22, 2014 at 9:35 AM, Björn Grüning bjoern.gruen...@gmail.com
wrote:
:) great I like it!
Will do it shortly!
Am 22.07.2014 15:36, schrieb Eric Rasche:
Apologies if this sounds like a basic question or if I am enquiring of the
incorrect list.
I have just had a local instance of galaxy installed on my MacPro.
Could somebody inform me of the best options for loading large BAM files (5Gb)
from the same hard drive into this instance of Galaxy. It
Set yourself as an administrator, and you can import the files
from disk (and link to them if you wish to avoid a copy) as part
of a data library. See:
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
Peter
On Tue, Jul 22, 2014 at 3:52 PM, Mark Lindsay
Hello everyone
I tried a galaxy update on my development instance of galaxy. It failed due to
a schema change coupled with a mysql version change. Don't worry about why it
failed - that has been resolved.
I have a backup copy of the database that I restored, which was based on schema
118. I
Your overall thought process seems correct. I suspect you still have a web
process for galaxy that is the only process being proxied by apache?
Make sure your universe_wsgi.ini has the option set to manage jobs in the
database (required for multiple handlers).
I would start with 8 handlers and
Thank you very much! I had a feeling about those 119_.pyc and 120_.pyc files
but I thought it recompiled on every launch and it would ignore them. I don’t
know much python
Regards,
Iyad Kandalaft
Microbial Biodiversity Bioinformatics
Agriculture and Agri-Food Canada | Agriculture et
For my part:Script/infra to generate brancheshttps://cpt.tamu.edu/gitlab/rasche.eric/docker-branch-generator/tree/masterGenerated branches:https://cpt.tamu.edu/gitlab/rasche.eric/generated-docker-branches/branches/recentNeed to patch up a couple issues, but I'm pretty much done on my end. Whenever
On Tue, Jul 22, 2014 at 7:51 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Jul 22, 2014 at 1:15 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Hi Peter,
On July 22, 2014 3:15:41 AM CDT, Peter Cock p.j.a.c...@googlemail.com
wrote:
Given how close you can get now for minimal effort,
Running jobs as the real user is not available with the PBS job
runner - one has to use the DRMAA interface to submit jobs as the real
user.
I have created a Trello card to add this functionality:
https://trello.com/c/OddS8bMP
Would be happy to field pull requests to add this - because I doubt
John,
How are those generated? Would you be amenable to scripting that portion and
running it once a month? (...say in a cron job, with a passwordless ssh key so
you never have to touch it again)
Cheers,
Eric
22.07.2014, 19:08, John Chilton jmchil...@gmail.com:
On Tue, Jul 22, 2014 at 7:51
Hey Eric,
This is not possible (easily anyway) in the latest release of blend4j.
It was on the TODO list though so I have added the functionality in
the following commit:
https://github.com/jmchilton/blend4j/commit/f92909fbda3616da09614b65810ebd86ce496b19
So instead of using
Hi John,
Okay, not a problem, no need to push new artifacts on my behalf.
Jetty (basically all of your dependencies) aren't currently ported to android
which puts that particular project on hold for me, for the time being.
Thanks for being aware of this issue.
Cheers,
Eric
22.07.2014, 21:10,
On Tue, Jul 22, 2014 at 3:13 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Hi John,
Okay, not a problem, no need to push new artifacts on my behalf.
Jetty (basically all of your dependencies) aren't currently ported to android
which puts that particular project on hold for me, for the time
Hello,
Thanks for the bug report. Is this on the main public server (usegalaxy.org)
or a local instance at the University of Iowa?
-John
On Wed, Jul 16, 2014 at 10:39 AM, Beck, Emily A emily-b...@uiowa.edu
wrote:
Hello,
I have repeatedly gotten the following error message when attempting
On Tue, Jul 22, 2014 at 7:41 PM, Eric Rasche rasche.e...@yandex.ru wrote:
John,
How are those generated? Would you be amenable to scripting that
portion and running it once a month? (...say in a cron job, with a
passwordless ssh key so you never have to touch it again)
Cheers,
Eric
How to
Howdy all,
This is probably only of interest to a tiny subset of you who work with
microscopy and microscope video, but I've added video datatypes and an
associated viz plugin for viewing .mp4 files.
Please feel free to submit bugs/feature requests/PRs on these
Hi Greg,
thanks for the clarification. Please see my comments below.
On Jul 20, 2014, at 3:22 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning bjo...@gruenings.eu wrote:
Hi,
single datatype definitions only work if you haven’t defined any
Hi Björn,
On Jul 22, 2014, at 6:01 PM, Björn Grüning bjoern.gruen...@gmail.com wrote:
Hi Greg,
thanks for the clarification. Please see my comments below.
On Jul 20, 2014, at 3:22 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning
Before we go too much further down this path with dataytpes, I'm wondering if
some of us should put together a spec of some kind that allows us to all agree
on the direction. For example, I'm wondering if datatyps should be versioned
and have a name-spaced identifier much like the Tool Shed's
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