November 2011 - galaxy-dev - lists.galaxyproject.org

Problem configuring local galaxy central installs and GATK beta pipeline
by Carlos Borroto 16 Nov '11

16 Nov '11

Hi, I noted there have been a change on the way GATK tools read picard_index.loc, from "tool_data_table_conf.xml":  <table name="gatk_picard_indexes" comment_char="#"> <columns>value, dbkey, name, path, tools_valid_for</columns> <file path="tool-data/picard_index.loc" /> </table> And I can't decipher how to use column "tools_valid_for". I was able to show selectable reference genomes in one of the tools by adding its id there, but I don't know how to add the rest. Should I separate them by spaces? commas? tabs?, none of these seem to work for me. Also, what is the best way to identify a tool id, should I just use file name for its xml file? Thanks in advance, Carlos

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Save These Dates! July 25-27: Galaxy Community Conference
by Dave Clements 15 Nov '11

15 Nov '11

Hello all, I am pleased to announce that the 2012 Galaxy Community Conference (GCC2012) has been scheduled for July 25-27, 2012 at the University of Illinois Chicago. See http://galaxyproject.org/wiki/Events/GCC2012 for more information on the meeting, and for sponsorship opportunities. Abstract submission and registration deadlines will be announced in the coming months. Please reserve July 25-27 on your calendar now, and hope to see you in Chicago next summer! Dave Clements PS: If your curious to know what goes on at a Galaxy meeting, see the GCC2011 page for an idea: http://galaxyproject.org/wiki/Events/GCC2011 -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Re: [galaxy-dev] Problem with the Galaxy tool shed
by Greg Von Kuster 15 Nov '11

15 Nov '11

Hello Marcel, This should now be working. The problem you encountered was due to the timeout setting in nginx being too short - this is fixed. In addition, I've added the ability to enter a URL into the upload form in the tool shed. I've also fixed several bugs, including renaming the repository and one related to deleting repository files. There are several other new features available as well - they'll soon be documented in the tool shed wiki. Let me know if you bump into any other problems. Thanks! On Nov 12, 2011, at 5:22 PM, Marcel Schumann wrote: > Hi Greg, > > ok, thanks. > Just for your information: uploading a relatively big package (approx. 15mb) worked previously for me without any problems. > > However, if you will implement some new package-update mechanism anyway, a very nice feature would be the support of downloads from remote servers (instead of upload from the local computer); just as the 'Upload File' tool allows to do in Galaxy. :-) > > > Best regards, > Marcel > > > On 11/12/11 10:18 PM, Greg Von Kuster wrote: >> Hi Marcel, >> >> Thanks very much for alerting me to the problem with the tool shed. I've got it functional again for the time being. I believe there's a problem with renaming a repository (which I'll fix asap) that caused the server error you saw. I'll also take a look at uploading your new version of your CADDSuite - I'm assuming we'll need to implement an ftp upload process because the browser may be timing out with the larger upload. I'll let you know what I find (I'll probably get back to you on Monday). >> >> Thanks again, >> >> Greg Von Kuster >> >> On Nov 12, 2011, at 11:58 AM, Marcel Schumann wrote: >> >>> Hi Dave, hi Greg, >>> >>> During the last few days, I tried several times to upload the current version of CADDSuite (1.0.1) to the galaxy tool shed; however, I always just got time-out errors. >>> >>> Now I have just had a look at the tool shed again, but most tool category can't even be viewed ('Server error'). So, is there any work with the tool shed server currently going on? Any reason why it can't work in the moment? ;-) >>> >>> By the way, if you (for debugging purposes) want to try to upload my packages yourself: >>> The packages are available from the project's homepage http://caddsuite.github.com >>> >>> https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.ta… >>> https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_MacOS_10.6.tar.… >>> >>> >>> Cheers, >>> Marcel >>> >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> > > > -- > Marcel Schumann > > University of Tuebingen > Wilhelm Schickard Institute for Computer Science > Division for Applied Bioinformatics > Room C313, Sand 14, D-72076 Tuebingen > > phone: +49 (0)7071-29 70437 > fax: +49 (0)7071-29 5152 > email: schumann(a)informatik.uni-tuebingen.de Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Galaxy Tool Shed used for main code hosting and collaborative development repo?
by Leandro Hermida 15 Nov '11

15 Nov '11

Hi, Quick question about the Galaxy Tool Shed, I would like to publish a tool suite there and wondering to people use the tool shed repositories as their main code hosting and development site or is it typical that people have their code hosted somewhere else a la Github or Sourceforge? regards, Leandro

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Actual User Code
by Chorny, Ilya 14 Nov '11

14 Nov '11

When I try to link file paths into a shared data library from the admin menu it fails. I get the following in the log file: galaxy.jobs DEBUG 2011-11-11 13:24:38,280 (2645) Changing ownership of working directory with: /usr/bin/sudo -E /home/galaxy/production/Sept06/galaxy-central/sc ripts/external_chown_script.py ./database/job_working_directory/2645 galaxy 504 galaxy.jobs ERROR 2011-11-11 13:24:38,771 fail(): Missing output file in working directory: [Errno 13] Permission denied: '/bioinfoSD/ichorny/test.bam' galaxy.datatypes.metadata DEBUG 2011-11-11 13:24:38,919 Cleaning up external metadata files STDOUT has the following : Job 2645's output dataset(s) could not be read Also my file get erased: /bioinfoSD/ichorny/test.bam Any thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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Galaxy in a frame?
by Oren Livne 14 Nov '11

14 Nov '11

Dear All, We are trying to integrate Galaxy with our web app, and we thought of having our web app as the main front end, and allow users to open an HTML frame with Galaxy in it within that app. However, Galaxy makes it impossible - it takes over the entire page when a user logs in or clicks on most links. Is it possible to embed Galaxy in another webapp or is it only designed as a standalone app? Thanks so much, Oren

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Timeout for job submission
by remy d1 14 Nov '11

14 Nov '11

Hello, In my configuration, I submit job through SGE. I have a cluster in the backend. If nodes are shutdown job is in state "queue wait" and I noticed that it disappear sometime. Is there a timeout somewhere in galaxy which is monitoring jobs ? In fact, I whish to use a script in SGE which is halting or booting nodes according to the SGE queue. -Regards Rem.

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only showing first lines of large output file
by Mattias de Hollander 14 Nov '11

14 Nov '11

Hello, I am observing some difficulties running a custom tool (processing an sff file). It shows up in Galaxy, runs and its three output files are given back. Only one of them is only showing the first 12 lines of many more... More symptoms: * The corrupted file is written successfully to disk as temp file in the galaxy tmp directory * Something goes wrong while transfering the file to the galaxy data dir (files/001), because while the tool is running the dataset_XX file is shown (as empty file), but after the other outputs are moved this file is gone * in galaxy only a snippet is shown, while the actual datafile is not on disk I would be happy to receive feedback on how to start debugging and solving this issue. Thanks! Mattias -- Bioinformatician Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands

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Re: [galaxy-dev] Configuration of a local install - mi-deploy ?
by Clare Sloggett 14 Nov '11

14 Nov '11

Hi Greg & Ross, Thanks for this! Yes, I confused the issue by mentioning the Tool Shed, sorry - it's the binaries themselves I need to install. Essentially I think I need to follow the steps at http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup , but I was wondering about mi-deployment scripts as a better way to do this, and whether that's standard practice. After looking through the scripts they really seem like the best option to me - it looks like they are set up so you mostly only need to change configuration variables to get this to work. The scripts are mentioned on the wiki instructions but don't seem to be the default option (they are not bundled in galaxy-dist), so I wondered if people are usually doing it this way? Thanks, Clare On Fri, Nov 11, 2011 at 2:06 AM, Ross <ross.lazarus(a)gmail.com> wrote: > Clare, > > As Greg says, the tool wrappers exposed on Main all come with a > mercurial checkout - but all the binary dependencies, genomic data and > indexes do not. The tool shed is really the tool-wrapper shed - binary > and data dependencies aren't there either. > > I haven't tried them but I'd guess that the deploy scripts take care > of a lot of messy details but will probably need some work to fit your > local setup. > > As to email for admin - my advice would be don't worry about it - if > one user forgets their password you can reset it from the admin > interface - that's the main use and if this is really a test instance, > it's not a show stopper. > > On Thu, Nov 10, 2011 at 9:14 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: >> Hello Clare, >> >> On Nov 9, 2011, at 11:11 PM, Clare Sloggett wrote: >> >>> Hi all, >>> >>> Most of our playing around with Galaxy has been in getting it working >>> on our local cloud, but now for the first time I'm configuring a >>> non-cloud local install of galaxy-dist (set up as per >>> http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server) >>> >>> So I have some naive questions! >>> >>> Would it be a sensible approach to grab the tools_fabfile script from >>> mi-deployment and use it in this case? Or should I be using the Tool >>> Shed for installing the base set of tools? >> >> >> The Galaxy distribution includes all of the tools you see on both the Penn State test and main instances. You can also get tools form the tool shed if you want - see our wiki at http://wiki.g2.bx.psu.edu/Tool%20Shed for information about how to do this. I don't think you'll need to use the tools_fabfile script from mi_deployment repo for your local instance. >> >> >>> >>> Also, if I have problems with this server sending out emails (which >>> may be the case) am I going to run into trouble with user/password >>> management or can I just admin everything manually? There will only be >>> a very small number of users on this server. >> >> I'm not clear on this question, but you certainly shouldn't run into any problems with user / password management within Galaxy. From the Galaxy Admin interface you have the ability to "Manage users" where you can reset passwords if necessary. >> >>> >>> If I have missed any good 'getting started' documentation on >>> config/admin of a local install please point me in the right >>> direction. I've been looking at http://wiki.g2.bx.psu.edu/Admin . >> >> You found the right wiki. >> >>> >>> Thanks, >>> Clare >>> >>> -- >>> E: sloc(a)unimelb.edu.au >>> P: 03 903 53357 >>> M: 0414 854 759 >>> ___________________________________________________________ >>> 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/ >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> >> >> ___________________________________________________________ >> 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/ >> > > > > -- > Ross Lazarus MBBS MPH; > Associate Professor, Harvard Medical School; > Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; > > > -- E: sloc(a)unimelb.edu.au P: 03 903 53357 M: 0414 854 759

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Problem with the Galaxy tool shed
by Greg Von Kuster 12 Nov '11

12 Nov '11

Hi Marcel, Thanks very much for alerting me to the problem with the tool shed. I've got it functional again for the time being. I believe there's a problem with renaming a repository (which I'll fix asap) that caused the server error you saw. I'll also take a look at uploading your new version of your CADDSuite - I'm assuming we'll need to implement an ftp upload process because the browser may be timing out with the larger upload. I'll let you know what I find (I'll probably get back to you on Monday). Thanks again, Greg Von Kuster On Nov 12, 2011, at 11:58 AM, Marcel Schumann wrote: > Hi Dave, hi Greg, > > During the last few days, I tried several times to upload the current version of CADDSuite (1.0.1) to the galaxy tool shed; however, I always just got time-out errors. > > Now I have just had a look at the tool shed again, but most tool category can't even be viewed ('Server error'). So, is there any work with the tool shed server currently going on? Any reason why it can't work in the moment? ;-) > > By the way, if you (for debugging purposes) want to try to upload my packages yourself: > The packages are available from the project's homepage http://caddsuite.github.com > > https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_Linux_x86-64.ta… > https://github.com/downloads/CADDSuite/main/CADDSuite_1.0.1_MacOS_10.6.tar.… > > > Cheers, > Marcel > Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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