Hi,
Is there a default notation to specify perl modules (threading modules)
in a tool configuration or in a submission to the toolshed?
I've got some tools to share that make extensive use of these modules,
and they are not default in a perl distribution. Hence, I'd like to
inform the users
Hi Geert,
Hi,
Is there a default notation to specify perl modules (threading modules)
in a tool configuration or in a submission to the toolshed?
I've got some tools to share that make extensive use of these modules,
and they are not default in a perl distribution. Hence, I'd like to
On Thu, Aug 1, 2013 at 12:11 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Dave,
The good news is it does seem some of the missing test results I
had on Monday have been resolved. However, there are still
others showing with no test results: :(
No test results here (I expect some to
Dear all,
I have a tool which contains the function A,B, and C, the output of
the function is the input of another function. I have developed a wrapper
for this tool using conditional tag to allow users select the function they
want. The label of the outputs (datasets) can be defined by
On Aug 7, 2013, at 7:55 AM, Jurgens de Bruin wrote:
Hi,
This is my first Galaxy installation setup so apologies for stupid questions.
I am setting up Galaxy on a Cluster running Torque as the resource manager. I
am working through the documentation but I am unclear on some things:
On Aug 7, 2013, at 9:23 PM, shenwiyn wrote:
Yes,and I also have the same confuse about that.Actually when I set
server:id in the universe_wsgi.ini as follows for a try,my Galaxy doesn't
work with Cluster,if I remove server:id,it work .
Hi Shenwiyn,
Are you starting all of the servers that
Dear Galaxy Community,
I have a local instance and installed 0.5.9-r16 BWA and the toolshed
wrapper. The mapping is successful. I then use the Filter Sam Tool on the
sam file from the alignment, but it spits out this error:
*Dataset 26: Filter SAM on data 24*
Tool execution generated the
Hello,
Could anyone tell me if there are detailed instructions anywhere for setting up
Galaxy on a Linux cluster using an LSF scheduler?
Thank you.
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and
To all,
I am getting the following error when I run sh run.sh :
galaxy.model.migrate.check DEBUG 2013-08-08 07:52:39,479 pysqlite=2 egg
successfully loaded for sqlite dialect
Traceback (most recent call last):
File
/scratch/sysusers/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py,
to add on this :
we have similar issues (sam-to-bam conversion fails with similar
errors). it seems to be related to the BWA output getting messed up,
with (part of) columns missing or duplicated on some lines.
I have not found a systematic pattern in the errors, they seem to happen
rather
Dear all,
When I try to run oasesoptimiser
https://galaxy.tamu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/oasesoptimiser/1.0.0
in Galaxy I get the following error:
Traceback (most recent call last):
File
Hello,
Can anyone tell me if there are detailed instructions anywhere for setting up
Galaxy on a Linux cluster using an LSF scheduler?
Thank you.
Ken.
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error
The issue here is the last line:
OperationalError: (OperationalError) disk I/O error u'PRAGMA
table_info(dataset)' ()
Do you have any security rules setup on the server, quotes, disk
issues, etc? You can always run a strace on run.sh for a better
understanding of whats going on.
--
Adam Brenner
Hello,
A naïve question, is it possible obtained from a galaxy-workflow a shell
script?, if yes, how can I do it?
Thank you in advance for your answer,
Victoria
___
Please keep all replies on the list by using reply all
in your mail
Hi Samuel,
On Wed, Aug 7, 2013 at 8:04 AM, Samuel Lampa samuel.la...@gmail.com wrote:
Thanks for the update, Dave!
Was delighted to see that the videos from all the talks (except lightning
talks) are up at:
On Jul 15, 2013, at 6:29 PM, Seth Sims wrote:
After some work i've created an Upstart script which can manage a load
balanced galaxy configuration as described in the wiki. I thought that I
would put it on this list for other people to use. The script parses
universe_wsgi.ini just like
On Aug 5, 2013, at 3:14 PM, David Hoover wrote:
Strangely, I had never noticed this before. On some tools, there is a link
at the top of the tool page that attempts to connect to
http://slyfox.bx.psu.edu:8080/, which it can't. This URL is set via the
qa_url directive in the
On Aug 5, 2013, at 6:23 PM, Rodolfo Aramayo wrote:
Hi,
I have a 80 core/1TB RAM Dell server.
In order improve Galaxy performance I modified the universe_wsgi.ini
file so as to improve the Scaling and Load Balancing
as follows:
# Use a threadpool for the web server instead of creating a
On Jul 26, 2013, at 3:51 PM, Leon Mei wrote:
Dear galaxy developers,
We have tried today to upgrade our proftpd configuration to make uploading
for our galaxy users possible again, both for users with old as well as
new style hashed passwords. We upgraded proftpd on the server to 1.3.5rc3
Hello dev-team,
I have updated
code repository
of our production instance https://galaxy.cbio.mskcc.org to the recent
galaxy-dist (10216:ebe87051fadf), now the instance page it is not rendering
in a proper way.
The error message I can see from the log file as follows:
On Jul 30, 2013, at 5:39 PM, Jim Johnson wrote:
I was using the quotas api to update a quota amount and got the error:
galaxy.web.framework ERROR 2013-07-30 15:40:59,149 Uncaught exception in
exposed API method:
Traceback (most recent call last):
File
On Aug 7, 2013, at 7:46 AM, Jasper Jan Koehorst wrote:
Hello,
I have a very simple jobrunner script that allows only 1 job to be run as
this galaxy is used for one thing in particular which consumes almost all
resources.
To do this I set the following:
plugins
plugin
I tried this method again and it still does not work. The only items in /mnt
are the directories cm and lost+found.
From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Thursday, August 01, 2013 4:48 PM
To: Ravpreet Setia
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re:
Anatoly, did this method work for you? It is not working for me.
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Dannon Baker [dannon.ba...@gmail.com]
Sent: Wednesday, August 07, 2013 8:00 PM
To: Ulyanov_Anatoly
Cc:
Ravpreet -- can you provide details as to what's failing for you?
If I remember correctly, you had an odd issue where nothing was actually
appearing at /mnt, right? This will not be the same issue as the tool
volume update.
On Thu, Aug 8, 2013 at 4:36 PM, Ravpreet Setia
Yeah, nothing happens after SGE gets to the running state. The directory
structure of the old ami does not appear in /mnt. The log was posted in the
following thread:
Cloudman - When will the symlinks be resolved ?
Additionally, I am not sure what you mean by, This will not be the same issue
On Thu, Aug 8, 2013 at 4:57 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote:
Yeah, nothing happens after SGE gets to the running state. The directory
structure of the old ami does not appear in /mnt. The log was posted in the
following thread:
Ahh, ok - I assumed since there was no
Initially Anatoly and I had the problem with the symlinks and were prescribed
the link to launch the old ami as a temporary solution until the latest ami
gets fixed. Thus I was curious if Anatoly would experience the same issue as me
when launching the older ami this way.
Anyways, I'll
In the form, under Instances in your account I choose New Cluster. Let me
know if there are additional details you need.
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Ravpreet Setia [ravpreet.se...@oicr.on.ca]
Sent:
Hello Dannon,
This bucket did not launch Galaxy properly. Here is the whole Cluster status
log:
22:11:22 - Master starting
22:11:23 - Completed initial cluster configuration. This seems to be a new
cluster; waiting to configure the type
22:11:27 - SGE prerequisites OK; starting the service
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