Hi --
I have an alignment job submitted to tophat using galaxy and the job
has said that it is waiting to start for the last day. My other jobs
have been running and completed and this has continued to be displayed
as waiting to run. Can you please help explain or address this?
Thank you,
--
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
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
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
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:
param name=paired_end label=This is paired end data type=boolean
truevalue=paired_end falsevalue=single_end checked=False/
Concretely,
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
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
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
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
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
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
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
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
-
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
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