Re: [galaxy-dev] No action for /admin_toolshed/prepare_for_install
by Greg Von Kuster
Hi Peter,
In your Galaxy install directory there will be a .hg subdirectory, and in that subdirectory there will be a file name hgrc. Yours probably looks something like this if you are tracking galaxy-dist.
[paths]
default = https://,your username.(a)bitbucket.org/galaxy/galaxy-dist
Just change the value of the path to track galaxy central:
[paths]
default = https://,your user name.(a)bitbucket.org/galaxy/galaxy-central
When you pull and update, you'll get the latest from galaxy central.
On Jul 10, 2012, at 6:13 PM, Peter van Heusden wrote:
> Hi Greg
>
> Is there any way to migrate from galaxy-dist to galaxy-central, or is a
> re-installation necessary?
>
> On 07/10/2012 11:56 PM, Greg Von Kuster wrote:
>> Hello Peter,
>>
>> To use the public Galaxy tool sheds, your local Galaxy instance must be running the tip from Galaxy central, not Galaxy dist. You need to be running at least 7368:3e6ab1cf0c2e, as this is the revision running on the public tool sheds. The public tool sheds always track the Galaxy central repository.
>>
>> Greg Von Kuster
>>
>>
>> On Jul 10, 2012, at 5:45 PM, Peter van Heusden wrote:
>>
>>> I am trying to install a tool (tmap_wrapper) from the Galaxy toolshed
>>> using the Admin interface to Galaxy. Unfortunately, each time I do this
>>> I get an error page with the message:
>>>
>>> No action for /admin_toolshed/prepare_for_install
>>>
>>> My Galaxy installation is galaxy-dist, revision 7148:17d57db9a7c0.
>>>
>>> Does anyone know why this might be happening?
>>>
>>> Thanks,
>>> Peter
>>>
>>>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
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>>> and other Galaxy lists, please use the interface at:
>>>
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>
>
10 years, 7 months
No action for /admin_toolshed/prepare_for_install
by Peter van Heusden
I am trying to install a tool (tmap_wrapper) from the Galaxy toolshed
using the Admin interface to Galaxy. Unfortunately, each time I do this
I get an error page with the message:
No action for /admin_toolshed/prepare_for_install
My Galaxy installation is galaxy-dist, revision 7148:17d57db9a7c0.
Does anyone know why this might be happening?
Thanks,
Peter
10 years, 7 months
Galaxy not killing split cluster jobs
by Peter Cock
Hi all,
We're running our Galaxy with an SGE cluster, using the DRMAA
support in Galaxy, and job splitting. I've noticed if the user cancels
a job (that was running or queued on the cluster) while the job is
shows as deleted in Galaxy, looking at the queue on the cluster
with qstat shows it persists.
I've not seen anything similar reported except for this PBS issue:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003633.html
When I don't use job splitting, cancelling jobs seems to work:
galaxy.jobs.handler DEBUG 2012-05-01 14:46:47,755 stopping job 57 in
drmaa runner
galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:47,756 (57/26504)
Being killed...
galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:47,757 (57/26504)
Removed from DRM queue at user's request
galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:48,441 (57/26504)
state change: job finished, but failed
galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:48,441 Job output not
returned from cluster
When I am using job splitting, cancelling jobs fails:
galaxy.jobs.handler DEBUG 2012-05-01 14:28:30,364 stopping job 56 in
tasks runner
galaxy.jobs.runners.tasks WARNING 2012-05-01 14:28:30,386 stop_job():
56: no PID in database for job, unable to stop
That warning comes from lib/galaxy/jobs/runners/tasks.py which starts:
def stop_job( self, job ):
# DBTODO Call stop on all of the tasks.
#if our local job has JobExternalOutputMetadata associated,
then our primary job has to have already finished
if job.external_output_metadata:
pid =
job.external_output_metadata[0].job_runner_external_pid #every
JobExternalOutputMetadata has a pid set, we just need to take from one
of them
else:
pid = job.job_runner_external_id
if pid in [ None, '' ]:
log.warning( "stop_job(): %s: no PID in database for job,
unable to stop" % job.id )
return
pid = int( pid )
...
I'm a little confused about tasks.py vs drmaa.py but that TODO
comment looks pertinent. Is that the problem here?
Regards,
Peter
10 years, 7 months
Installation on HPC and file upload
by Lee Hazelwood
Dear developers,
I'm wondering if you might be able to help us with an issue with have at Leeds. We have installed the galaxy platform on our HPC cluster at Leeds. One issue we have is uploading files > 2 GB through the internet browser. We have tried the URL route also without success. Are there any solutions to this problem?
One idea we had was whether it is possible to change the upload to look at the filesystem local to galaxy rather than the users own computer.
Many thanks
Lee
--
Dr Lee Hazelwood
BHRC Bioinformatics Technology Group Leader
Biomedical and Health Research Centre
Faculty of Biological Sciences and
Leeds Institute of Molecular Medicine
University of Leeds,
Leeds,
LS2 9JT, UK.
E-mail: L.D.Hazelwood(a)leeds.ac.uk<mailto:L.D.Hazelwood@leeds.ac.uk>
http://www.bhrc.ac.uk/initiatives/technology-groups/bioinformatics-techno...
10 years, 7 months
Re: [galaxy-dev] Job output not returned from Cluster
by Sascha Kastens
Hi Hemant,
thanks for your help. I have set the value to 100, but this did not fix the problem.
I am now trying to get a NFS mounted with -noac.
Cheers,
Sascha
Original Message
processed by CONSOLIDATE
Subject:
RE: [galaxy-dev] Job output not returned from Cluster
Sent:
Montag, 9. Juli 2012 17:38
From:
Kelkar, Hemant (hkelkar(a)unc.edu)
Hi Sascha,
I am not sure if the error you are seeing is like one I had posted in this thread? http://dev.list.galaxyproject.org/Problem-related-to-a-job-that-quot-fail...
--Hemant
From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Sascha Kastens
Sent: Monday, July 09, 2012 11:26 AM
To: galaxy-dev(a)lists.bx.psu.edu
Subject: Re: [galaxy-dev] Job output not returned from Cluster
Hi!
Unfortunately I was not able to fix this problem yet.
Is anybody out there who had a similar problem while using Galaxy with SGE or has the knowledge about the things I can look at?
Thanks in advance!
Cheers,
Sascha
10 years, 7 months
Automating customized setup of cloudman galaxy
by Dave Lin
Dear Galaxy Dev Team-
I'm looking to automate the complete setup/build of a customized galaxy
cluster from the command line.
I'm looking for help/suggestions on several steps (labeled MANUAL) where it
currently requires manual ui-input
1) [Automated] Have a script that uses cloudman + ec2-api-tools to create
new galaxy cluster on Amazon from scratch.
2) [MANUAL] open browser to the new instance, enter volume size and start a
new cluster. (Looking to be invoke this via command-line)
3) [MANUAL] Create standard users via the galaxy ui. (looking to be able
to create a few standard users via command-line, not UI)
4) [MANUAL] Update galaxy to galaxy-dev tip using the galaxy-ui. (Can I
just run hg pull/update? There doesn't seem to be the mercurial metadata in
the galaxy-central directory.)
5) [Automated] Pull custom code from personal bitbucket, apply changes,
create missing directories, install tools, etc. Copy over various configs
(toos_conf.xml , universe_wsgi,etc)
6) [MANUAL] Import each workflow using the galaxy UI. (Have several
workflows, and currently have to manually import them via the UI. I'm
looking to make some type of command-line/api call that can pass the
workflow to galaxy)
I could go into the code and figure out how to call these functions or
possibly just insert rows into the database. However, I'm looking to
approach this using more official/supported API's.
Would be happy to try to contribute/document this process once I have it
working if others are interested.
Thanks in advance,
Dave
10 years, 7 months
Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10
by Dorset, Daniel C
________________________________________
From: galaxy-dev-bounces(a)lists.bx.psu.edu [galaxy-dev-bounces(a)lists.bx.psu.edu] On Behalf Of galaxy-dev-request(a)lists.bx.psu.edu [galaxy-dev-request(a)lists.bx.psu.edu]
Sent: Saturday, July 07, 2012 11:00 AM
To: galaxy-dev(a)lists.bx.psu.edu
Subject: galaxy-dev Digest, Vol 73, Issue 10
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2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.
Today's Topics:
1. pbs_python issues (Iry Witham)
2. Which css file does welcome.html use? (Dorset, Daniel C)
3. Re: Which css file does welcome.html use? (Jeremy Goecks)
Hi Ira,
I'm in charge of a Galaxy instance that's also deployed on a PBS Cluster, and I went through this process a couple of months ago. If I remember correctly, when you run your Python script, you're supposed to run it with "-e" not "?e" Assuming that you are pointing to the correct directory, it looks like everything else about your command is correct.
Have you tried that?
----------------------------------------------------------------------
Message: 1
Date: Fri, 6 Jul 2012 16:32:14 +0000
From: Iry Witham <Iry.Witham(a)jax.org>
To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu>
Subject: [galaxy-dev] pbs_python issues
Message-ID: <CC1C8B4D.8EAD%iry.witham(a)jax.org>
Content-Type: text/plain; charset="windows-1252"
I am having an issue with pbs_python loading, but not submitting jobs to the cluster.
The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py ?e pbs_python' it failed to generate the pbs_python egg in the /galaxy-dist/eggs/ directory.
Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from my production galaxy server and restarted my test server. It appears to start, but when I attempt to run anything it uses the local runner and fails. The runner0.log shows the pbsjobrunner is loaded is below:
galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner: galaxy.jobs.runners.pbs:PBSJobRunner
galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue started
galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue started
galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue started
galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue started
I can't seem to get past this point since I upgraded. Can someone point me in the right direction?
Thanks,
Iry
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10 years, 7 months
Galaxy Czars: Doodle pool for first Teleconference
by Ann Black-Ziegelbein
Hi everyone -
We are targeting a web conference call for Galaxy Deployers/Operators
for July 9th or 10th. This teleconference will be held using Elluminate
Live/Blackboard Collborate web conference - so all data (including
voice) will be over the internet. We have good luck at the University
of Iowa with this technology for world wide remote conferences (our
Ponseti International group uses it for their large distributed
collaboration and others) and we can record our session and post it for
playback off of the wiki.
Finding a time that will suit everyone will be a challenge. If you can
take a moment to respond to the doodle poll with when you can join a web
conference, it will help us find the best time for the majority:
http://www.doodle.com/f4f2f37smgcv3z6n
By the way, if you have not found it yet, here is a link the Galaxy Czar
wiki page:
http://wiki.g2.bx.psu.edu/Community/GalaxyCzars
Here is a draft agenda for our first call - comments are welcome :
*For our first Mtg.*
* Logistics: Address how we want to tackle these calls. Go over generic
agenda. Frequency of calls
* Presentation: Galaxy at Iowa: Discuss our issues with big data, how
NGS tools take in/output data and finding the right storage server solution.
* Group Goals: what do we want to accomplish with this group beyond
discussions/sharing?
* Open Mic & recruit new volunteers for the next call.
*My shot at a generic agenda outline - to be customized each User Group
Mtg ?
*
20 min: Galaxy in Our Town. - presentation from a local galaxy
institution on what they are doing or a problem they are troubleshooting
- or have someone walk through their use cases and pain points.
20 min: Galaxy Today/Tomorrow. - presentation on a galaxy coding item.
Either from penn state team, or from someone working on a new feature or
customization.
20 mins: Open Mic Discussion & make point to point connections. IE -
organize smaller breakouts if someone wants to host a call specific to
an issue.
Thanks everyone!
Ann
10 years, 7 months
Re: [galaxy-dev] galaxy-dev Digest
by Irene Bassano
Hello there,
Hope this is the right mailing list.
Where can I find a detailed explanation of the "track" options when selecting a particular "group" in the UCSC main Table Browser. E.g: If I choose "group: "Genes and gene prediction track", what is the difference between the various tracks listed?
The UCSC website does not give a detailed explanation of the differences between the various options. And outputs change depending on this.
Thanks,
Irene
--------------------------
Irene,
What you want is a tutorial for the UCSC table browser. Something like this will help:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
Clicking on the button 'describe table schema' provides additional information about the tracks's content.
In the future, please email the galaxy-user mailing list with questions such as these. This email list goes to the entire Galaxy team and community, so you're likely to get quicker and more complete replies there.
http://wiki.g2.bx.psu.edu/Mailing%20Lists
Best,
J.
On Jul 8, 2012, at 6:28 AM, Irene Bassano wrote:
Hi Jeremy,
I am new with the Galaxy system and I was wondering if there is a web site which explains the possible options listed in "group" and "track" when loading data from UCSC.
Depending on the group, the track changes: is there any manual that explains the difference between all these options?
Many thanks,
Irene
________________________________________
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Sent: Sunday, July 08, 2012 5:00 PM
To: galaxy-dev(a)lists.bx.psu.edu
Subject: galaxy-dev Digest, Vol 73, Issue 11
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Today's Topics:
1. Re: galaxy-dev Digest, Vol 73, Issue 10 (Dorset, Daniel C)
2. How to add tag in tool xml file (sshashi)
----------------------------------------------------------------------
Message: 1
Date: Sat, 7 Jul 2012 14:10:45 -0500
From: "Dorset, Daniel C" <daniel.dorset(a)Vanderbilt.Edu>
To: Iry Witham <Iry.Witham(a)jax.org>
Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu>
Subject: Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10
Message-ID:
<9B568B41976B54469CC6E3FD758EF83105DBFE7C24(a)ITS-DRWNEM10.ds.Vanderbilt.edu>
Content-Type: text/plain; charset="us-ascii"
________________________________________
From: galaxy-dev-bounces(a)lists.bx.psu.edu [galaxy-dev-bounces(a)lists.bx.psu.edu] On Behalf Of galaxy-dev-request(a)lists.bx.psu.edu [galaxy-dev-request(a)lists.bx.psu.edu]
Sent: Saturday, July 07, 2012 11:00 AM
To: galaxy-dev(a)lists.bx.psu.edu
Subject: galaxy-dev Digest, Vol 73, Issue 10
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To subscribe or unsubscribe via the World Wide Web, visit
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When replying, please edit your Subject line so it is more specific
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HEY! This is important! If you reply to a thread in a digest, please
1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread.
2. Strip out everything else in the digest that is not part of the thread you are responding to.
Why?
1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.
Today's Topics:
1. pbs_python issues (Iry Witham)
2. Which css file does welcome.html use? (Dorset, Daniel C)
3. Re: Which css file does welcome.html use? (Jeremy Goecks)
Hi Ira,
I'm in charge of a Galaxy instance that's also deployed on a PBS Cluster, and I went through this process a couple of months ago. If I remember correctly, when you run your Python script, you're supposed to run it with "-e" not "?e" Assuming that you are pointing to the correct directory, it looks like everything else about your command is correct.
Have you tried that?
----------------------------------------------------------------------
Message: 1
Date: Fri, 6 Jul 2012 16:32:14 +0000
From: Iry Witham <Iry.Witham(a)jax.org>
To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu>
Subject: [galaxy-dev] pbs_python issues
Message-ID: <CC1C8B4D.8EAD%iry.witham(a)jax.org>
Content-Type: text/plain; charset="windows-1252"
I am having an issue with pbs_python loading, but not submitting jobs to the cluster.
The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py ?e pbs_python' it failed to generate the pbs_python egg in the /galaxy-dist/eggs/ directory.
Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from my production galaxy server and restarted my test server. It appears to start, but when I attempt to run anything it uses the local runner and fails. The runner0.log shows the pbsjobrunner is loaded is below:
galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner: galaxy.jobs.runners.pbs:PBSJobRunner
galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue started
galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue started
galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue started
galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue started
I can't seem to get past this point since I upgraded. Can someone point me in the right direction?
Thanks,
Iry
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
10 years, 7 months
Adding a new tag in galaxy
by sshashi
Hi All,
I installed galaxy on local machine and i want to add a new tag in tool
xml file .docs for adding new tag is not available in galaxy .if any
one is working on it, plz help me in finding the solution ..
Regards
shashi
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10 years, 7 months
