Hi Jennifer,
Today I was trying to pull some bowtie2 indices from Galaxy rsync server for
PhiX to run some tests and just got the ones for bowtie1… I'm wondering what's
the state in regards to this past thread and what we can do to help in here.
Cheers!
Roman
7 mar 2013 kl. 20:01 skrev
Hello Galaxy!
I can actually confirm this issue in my macbook air after fetching a fresh
clone from galaxy-dist (a few minutes ago) and running a:
$ rm -rf eggs/* ./run.sh
(… many correctly fetched eggs… )
Traceback (most recent call last):
File ./scripts/fetch_eggs.py, line 37, in module
Hello Brad, Jennifer,
I'm also interested in this initiative since I'm using Brad's code as
a part of a testsuite for a bloom filter:
https://github.com/SciLifeLab/facs/blob/master/facs/utils/galaxy.py
As both of you pointed out, there's a need for some cleanup, there are
some stray files here
Chorny,
We had a similar issue with slurm-drmaa, and we exchanged some emails
with the upstream drmaa maintainer (Mariusz, also reading this list).
At the end he decided to export the environment variables from the
submitting node shell to the worker nodes. That solves the problem in a
more
: University of Dundee
To: Roman Valls brainst...@nopcode.org
Hi,
The SGE_ROOT variable was the same as always, but it turns out I had a
DRMAA_LIBRARY_PATH path that was still pointing to the old path. It's
such a long time since I set up galaxy that I'd forgotten about it.
Changed it and Galaxy
Hey Nate,
On 2011-08-16 20:21, Nate Coraor wrote:
Roman Valls wrote:
Thanks indeed for the ~/.slurm_drmaa.conf hint Mariusz, very useful !
I wonder how this approach will work out when one runs galaxy as advised
in a production setting:
http://usegalaxy.org/production
Together
Thanks indeed for the ~/.slurm_drmaa.conf hint Mariusz, very useful !
I wonder how this approach will work out when one runs galaxy as advised
in a production setting:
http://usegalaxy.org/production
Together with the gordon patch to run drmaa as different users:
, Roman Valls brainst...@nopcode.org wrote:
Hi Liu,
Does your app execute Picard/GATK at some point ? In that case those
would be the ones triggering your Java OOM error, in that case Bo's
suggestion is the way to go. That's my best guess since Galaxy itself
doesn't use java either (only
Sorry for the cross-posting, but I guess that's also interesting to
Galaxy users...
I've been thinking about input validation too... only a bit more
generally, on a server/production basis. Nate, on your production
setup[1] (galaxy main), do you use any kind of filter or framework a la
Sorry for the cross-posting, but I guess that's also interesting to
Galaxy users...
I've been thinking about input validation too... only a bit more
generally, on a server/production basis. Nate, on your production
setup[1] (galaxy main), do you use any kind of filter or framework a la
Hi Liu,
Does your app execute Picard/GATK at some point ? In that case those
would be the ones triggering your Java OOM error, in that case Bo's
suggestion is the way to go. That's my best guess since Galaxy itself
doesn't use java either (only python AFAIK).
Regards,
Roman
On 2011-06-27 18:44,
Nate, is it just me or all the .png links on that wikipage are
broken/missing ? :-S
On 2011-05-26 10:38, Nate Coraor wrote:
Duddy, John wrote:
We'd like to be able to associate fixed things (project, Sample, sequencer
used) with user's FASTQ files, and we'd also like to allow users to
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