Dave,
I upgraded the galaxy to Sep 7 release. The KeyError error has gone as
expected.
But the deferred_job_queue error persists. We are running galaxy in the
cluster (SGE) here. Is it possible that Manage local data need to be
configured in the cluster env?
Regards,
Derrick
On Mon, Sep 10, 201
Hi everyone!
We are targeting a web conference for our second Galaxy Deployers/Operators
group meeting for the last two weeks of September. The time we set for the
September meeting I would like to use as a template for future meetings.
(EG 3rd Monday at 9 am central time). Please take a moment
Hi all,
Could someone please point me to helpful ressources for installing HYPHY in
Galaxy?
- I've downloaded, compiled and installed HyPhy
- I've copied the contents of the installation folder to
.../galaxy-dist/tool-data/HYPHY
- I've symlinked HYPHYMP in that folder to HYPHY
- I
Hi Dave,
The enable_beta_job_managers is set to true in my universe ini file.
Unless it can be override in somewhere else?
My galaxy hasn't been patched to the Sep release, but will give it a try.
I actually also downloaded the complete pre-built indexes from galaxy's
recent released rsync serv
Hi,
I have a very recent version of Galaxy installed locally, and when I run
FastQC:Read QC, it creates an HTML file with missing links to the plots and
images within the HTML. The HTML source looks identical to the HTML source
from the main Galaxy server, so there must be something wrong with
i use a cron job to monitor my disks and email me if they approach capacity.
i'm not sure of the benefit of informing your users; better for a sysop to
take care of it before it becomes a problem.
i also use cron jobs to purge older files from the ftp and tmp dirs.
On Thu, Sep 6, 2012 at 6:48 AM,
I downloaded the latest galaxy-dist this morning and I used the test toolshed
to test my repository first before I upload it to the main toolshed.
Thanks
Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics,
Inc.
(650) 428-6023 office | (408) 605-3938 mobile
bcr...@compl
Hello Birgit,
It looks like you are attempting to install from the test Galaxy tool shed,
which tracks fairly closely to the Galaxy central repository on bitbucket.
What changeset revision of Galaxy are you running? It will always speed up our
handling of issues like this if you include this
Hi Bjorn,
The main Galaxy tool shed is tracking the Galaxy-dist repository. Per requests
from the Galaxy community, it no longer tracks Galaxy-central.
Greg Von Kuster
On Sep 10, 2012, at 12:25 PM, Björn Grüning wrote:
> Hi,
>
> the toolshed is not starting with the latest galaxy-central ver
Hi,
the toolshed is not starting with the latest galaxy-central version.
Attached is a small patch to solve that problem.
Cheers,
Bjoern
--
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freib
Hello,
We noticed a problem with the tool Filter Fastq. It seemed to mishandle the
paired-end checkbox. Here is the XML which seems to not work:
Concretely, $paired_end.value return True or False as value and not
"paired_end" or "single_end", so in the python code execution,
#if
Hi Nikhil,
Purging datasets is covered in the Galaxy Wiki.
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Purge%20Histories%20and%
20Datasets
Basically, there's a bunch of scripts in
{GALAXY_HOME}/scripts/cleanup_datasets/ that require running.
We've created a single .sh file that executes
Hi Suzan,
The problem here is that there's an absence of data for one of the genes
you want to compare, so one can't really assign any significance to that
particular gene or transcript.
This would require inventing a singificance value where if a gene is
highly expressed in one sample, but not mea
Derrick,
The deferred_job_queue instance in the job manager object is only
instantiated when the enable_beta_job_managers variable is set to True.
Is it possible that your previous setting of that variable was somehow
reverted?
The KeyError error you mentioned in your previous should be fixe
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