Hi,
We’re having a bit of an error where the GUI shows that a job had an error.
When the user submits the job, the job is seen to have run via terminal and
uge. The job working directory exists and the out and error file is in there.
Once the job completes, it seems like the GUI will say that i
Hi all,
We’re having a bit of trouble with a local version of Galaxy where all the
tools that were installed via tool shed is showing an uncaught error on the
user interface.
The tools have clearly been installed and can be seen in the admin panel on the
interface as well as the psql database
Hi all,
When attempting to start up Galaxy, via the run.sh script, we’re getting the
following error:
galaxyd@genomics:/galaxy$ sh run.sh
Activating virtualenv at .venv
Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages
Double requirement given: Tempita==0.5.3.dev0 (f
Hi John,
Thanks for the reply. I saw in the stack trace that there was a issue with
mercurial, which was recently installed in the system. After uninstalling it,
everything ran again. Not entirely sure what happened.
Thanks,
Miuki
On Mar 14, 2017, at 8:27 AM, John Chilton
mailto:jmchil...@gmai
Hi all,
This afternoon, our local instance of Galaxy suddenly started producing errors
for all jobs. This is the trace that gets printed out. Not sure what is
happening because the error doesn’t give much information other than python not
being able to find a module.
Traceback (most recent cal
Hi all,
Is Torque still supported as a resource manager?
This page ( https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster )
mentioned the usage of Torque and how to set it up. However, the setup
instructions refer to a /script/scramble.py file which I assume interfaces with
eggs. If
Hi all,
Is there a way to restart Galaxy without having to wait till all the
outstanding jobs are finished running? I’ve noticed that whenever Galaxy daemon
is stopped and then started, the UI does not return back online until all the
jobs that were running are finished or killed because they a
Hi all,
After setting up AD/LDAP in Galaxy, we noticed that for some reason, some users
are able to log in but others were not. We don’t think that it has anything to
do with the set up of LDAP or AD at our institute and we’ve tried to find
common threads between the users who can log in but we
Hi all,
After installing the following devteam tools from the ToolShed: Base
Coverage/Cluster/Complement/Concatenate/Flanking_features/get_flanks/Intersect/Join/Merge/Subtract
The tools give an error after being run.
Traceback (most recent call last):
File
"/galaxy/shed_tools/toolshed.g2.bx.
Hi all,
When a tool is installed onto Galaxy via the GUI from the ToolShed, where is
the tool itself installed on the system?
For instance, having installed Bed Tools from the ToolShed, the tool errors out
on a run with the following error:
Fatal error: Exit code 127 ()
/galaxy/database/job_wo
s/3084
>
> More good news: This will likely be fixed in the next release
> of Galaxy:
>
> https://github.com/galaxyproject/galaxy/pull/3122
>
> Right now I suggest you manually edit these XML files to
> use the word "and" instead of "&".
>
&g
panel.xml file has some problems.
> Can you try to move this file to a different location and try the
> installation again?
> It should be located in your galaxy directory.
>
> Best,
> Marius
>
>
> On 11/03/2016 03:16 PM, Yip, Miu ki wrote:
>> Hi all,
>>
&
Hi all,
While trying to install tools from the toolshed via the browser interface, an
error keeps appearing and nothing is abled to be installed. Currently using the
latest version of Galaxy and having tried to install several different tools,
the following error keeps appearing in the log file
Hi all,
When trying to submit a job to the cluster via Pulsar from Galaxy, an error is
thrown and the job won’t be submitted.
The paster.log file has the following error:
Exception: Attempt to use DRMAA, but DRMAA Python library cannot be loaded.
OSError - problem loading shared library [/opt/u
Hi all,
I’m trying to import shed tools into Galaxy for Docker. When I build the
container, I get this error message:
TASK [galaxy_tools : Install Tool Shed tools] **
[WARNING]: The loop variable 'item' is already in use. You should set the
`loop_var` value in th
Hi,
I’m trying to configure a new instance of Galaxy and I want to use LDAP for
user authentication. I have taken a look at this wiki page:
https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth
I followed the instructions and when I looked into the auth_conf.xml file, I
was unsure of wh
Hi,
I ended up getting nginx running. Turns out it was just a selinux issue.
Thanks and sorry for the trouble!
Best,
Miuki
From: Yip, Miu ki
Sent: Thursday, July 28, 2016 4:28 PM
To: galaxy-dev@lists.galaxyproject.org
Subject: Galaxy in Docker and nginx
Hi
Hi Galaxy Team,
I'm currently trying to use Galaxy in Docker, and I wanted to know if there are
special actions that I have to do in Galaxy for nginx. I'm trying to set up a
reserve proxy and have url forwarding. Do I need to inform Galaxy in Docker
that nginx is being use?
Thanks,
Miuki
_
tself when I
attach.
Thanks so much,
Miuki
From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Wednesday, July 20, 2016 2:05 PM
To: Yip, Miu ki; Björn Grüning; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Galaxy, Docker Containers, and Installin
iables are stored for docker Galaxy? I have tried looking for an
env file, but could not find it.
Thanks so much!
Miuki
From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Wednesday, July 20, 2016 2:23 AM
To: Yip, Miu ki; galaxy-dev@lists.galaxyproject.org
S
Hello Galaxy Team,
We're from the Bioinformatics Shared Resources at Cold Spring Harbor Lab and
we're trying to create a new flavour of Galaxy for local use in the lab using
docker containers.
We want to add tools that are specific for our lab, such as importing files
from our system, onto thi
Hello Galaxy Team,
We're from the Bioinformatics Shared Resources (BSR) at Cold Spring Harbor Labs
and we're looking to implement irods on a newly installed version of Galaxy.
We want to incorporate iRODS (http://irods.org/). Is there a recommended way to
do this, or no?
Thanks in advance for
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