On Tue, Oct 7, 2014 at 1:47 AM, Isabelle Phan
isabelle.p...@seattlebiomed.org wrote:
Hello,
I installed clustalomega from the galaxy main toolshed using the admin
interface of our local galaxy install.
When I run the tool, I get this message:
Dataset generation errors
Dataset 55:
Dear all
Maybe one of you can shed some light on this error message that I see in
the log file for one of my handler processes. I get about one of them
per second. The effect is that most of the jobs remain in the waiting
to run stage.
The postgres database is running on a separate server and
Hi Dannon
I am running 6 handler and 6 web processes. I have the latest stable
version of the code (from June 2nd 2014). My postgres database (version
8.4.9) is running on a different server on the same subnet. Both servers
are Centos (6.5 on the Galaxy server, 6.2 on the database server).
Update:
The usual switching it off and on again (server reboot) has resolved the
problem (for now), albeit in a rather unsatisfactory manner.
If there are any insights what caused this behaviour and how it can be
avoided in the future I'd be more than happy to hear them.
Cheers
Ulf
On
Hi all,
I'm trying to install R/bioconductor packages in galaxy and have trouble
with some of them.
I made a dependency package (package_qdnaseq_1_0_5 in the
testtoolshed) that should install several R (bioconductor) packages
using setup_r_environment and for each package the
I don't believe I received any replies to this, so I will answer my own
question for the benefit of others who might run into this problem.
It seems that the tool shed is being served over HTTP SSL now and traffic over
HTTP without SSL is being redirected. My tool_sheds_conf.xml defines the
Hi Enis,
Thanks for that information. Now I am getting an error with the
Unified_Genotyper failing to locate the GenomeAnalysisTK.jar. I discovered
that gatk2 needs to be downloaded and installed. I have done that, but can't
seem to figure out where the env.sh file reference below exists.
I'm having trouble after setting up SSL on our Apache proxy for Galaxy.
When I try to import data from UCSC, Galaxy tries to go to the http
(non-ssl) url for UCSC and thus generates a security error in the
browser and the request is blocked. I have added
RequestHeader set X-URL-SCHEME
Hi folks,
Got a strange problem - it's hit me on all my self-install options today
including using the Chef cookbook as well as the galaxy mecurial install
method on Ubuntu 12.04 LTS
I'm trying to build a local galaxy that supports a few common extra
tools (things like samtools etc.)
I can
Hi Chris,
(1) Galaxy configuration has been moved to /config/galaxy.ini
(
https://bitbucket.org/galaxy/galaxy-dist/src/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb/config/
)
(2) There might have been some changes to the conf syntax regarding the
dependency directory etc. since the version of
Thanks Peter. You guessed correctly, I tried
https://toolshed.g2.bx.psu.edu/view/clustalomega/clustalomega ... I'm back
to using the command line ;-)
cheers,
Isabelle
On 10/7/14 1:45 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Oct 7, 2014 at 1:47 AM, Isabelle Phan
Thanks for the rapid reply!
Right now I'm thinking that my toolshed issues are caused by the HTTP to
HTTPS redirects on the main tool shed servers. I've set the URL to use
https in the tool_sheds_conf.xml page and we'll see how far I can get ...
Regards,
Chris
Martin Čech wrote:
Hi Chris,
Martin Čech wrote:
(2) There might have been some changes to the conf syntax regarding the
dependency directory etc. since the version of universe.wsgi.ini that
you are using. So please make sure you are using the current galaxy.ini
file and try installing a tool again. If it does not go
Hi Iry,
Yeah, I see what you mean about that *env.sh* file not being in the GATK2
repo the readme states so. I'm not sure what's exactly supposed to be in
that file for GATK2 in particular so perhaps one of the wrapper authors can
jump in. For majority of tools, you'd just need something like this
Jumping in ;)
Hi Iry,
please have a look at our small readme file under:
https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2
The problem is that we are not allowed to ship the jar file. So we came
up with the idea to provide you with empty env.sh file you need to edit.
Sorry
I am trying to reset metadata on all my repositories at once using the
Reset metadata on my repositories button on
https://testtoolshed.g2.bx.psu.edu/ It fails with:
Internal Server Error
Galaxy was unable to successfully complete your request
URL:
Hi Lyad and John,
Thanks for your replies and sorry for my no detailed question.
Well, I'm developing a tool that is applied to analyse PDB files
(proteomics stuffs) ,compare them, and create a ranking sort by the best
solutions (PDB files), making some graphs and 3D images. This tool will
have
Seems like missing import:
from galaxy.model.orm import or_
I will check on it tomorrow as a whole.
Thanks for reporting this.
M.
On Tue, Oct 7, 2014 at 7:03 PM, Saket Choudhary sake...@gmail.com wrote:
I am trying to reset metadata on all my repositories at once using the
Reset metadata
Hi All,
The October Galaxy newsletter went out a week ago. Buried at the bottom is
this
-
36 new ToolShed repos
https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions
which lists repositories that have been published in the Galaxy Project
ToolShed in the
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