July 2012 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] No action for /admin_toolshed/prepare_for_install
by Greg Von Kuster 10 Jul '12

10 Jul '12

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" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ > >

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No action for /admin_toolshed/prepare_for_install
by Peter van Heusden 10 Jul '12

10 Jul '12

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

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Galaxy not killing split cluster jobs
by Peter Cock 10 Jul '12

10 Jul '12

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

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Installation on HPC and file upload
by Lee Hazelwood 10 Jul '12

10 Jul '12

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-technolo…

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Re: [galaxy-dev] Job output not returned from Cluster
by Sascha Kastens 10 Jul '12

10 Jul '12

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-failed… --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

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Automating customized setup of cloudman galaxy
by Dave Lin 09 Jul '12

09 Jul '12

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

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Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10
by Dorset, Daniel C 09 Jul '12

09 Jul '12

________________________________________ 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 Send galaxy-dev mailing list submissions to galaxy-dev(a)lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request(a)lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-owner(a)lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." 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.

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Galaxy Czars: Doodle pool for first Teleconference
by Ann Black-Ziegelbein 09 Jul '12

09 Jul '12

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

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Re: [galaxy-dev] galaxy-dev Digest
by Irene Bassano 09 Jul '12

09 Jul '12

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 ________________________________________ 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: Sunday, July 08, 2012 5:00 PM To: galaxy-dev(a)lists.bx.psu.edu Subject: galaxy-dev Digest, Vol 73, Issue 11 Send galaxy-dev mailing list submissions to galaxy-dev(a)lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request(a)lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-owner(a)lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." 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. 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 Send galaxy-dev mailing list submissions to galaxy-dev(a)lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request(a)lists.bx.psu.edu You can reach the person managing the list at galaxy-dev-owner(a)lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." 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.

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Adding a new tag in galaxy
by sshashi 09 Jul '12

09 Jul '12

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 ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. -------------------------------------------------------------------------------------------------------------------------------

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