galaxy-dev February 2011

galaxy-dev@lists.galaxyproject.org

63 participants
110 discussions

March 2011 GMOD Meeting early registration closes this Friday
by Dave Clements 14 Feb '11

14 Feb '11

Hello all, *Register for the March 2011 GMOD Meeting ( http://gmod.org/wiki/March_2011_GMOD_Meeting) by this Friday, Feb 18, and save over 15%.* The March meeting is part of GMOD Americas 2011 ( http://gmod.org/wiki/GMOD_Americas_2011), an event that includes Satellite Meetings, a GMOD Course (already full), and for the first time, an "Introduction to GMOD" session the night before the meeting for GMOD newcomers. GMOD Americas 2011 events are being held at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States. Also, if you have a topic you want to discuss at the meeting, please send it to Scott Cain <scott(a)scottcain.net> ASAP so he can get you on the program. *About GMOD:* GMOD is the Generic Model Organism Database project, a collection of interoperable open-source software components for annotating, visualizing, managing and analyzing biological data. GMOD is also an active community of software developers and biologists addressing common challenges with their data. The GMOD suite includes widely used tools such as GBrowse and JBrowse (and WebGBrowse) for genome browsing, Apollo and MAKER for genome annotation, GBrowse_syn and CMap for comparative genomics visualization, Chado, BioMart and InterMine for data integration, management, and querying, and Galaxy and Ergatis (and ISGA) for data analysis. *Meeting Overview: *As with previous GMOD meetings, this meeting will have a mixture of project talks, component talks, and user talks. Our guest speaker is Dr. Eric Stone of North Carolina State University. Dr. Stone will talk about his experience on the "Drosophila Genome Reference Panel," a project that is sequencing and annotating almost 200 inbred lines. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now. For an idea of what happens at a GMOD meeting, see the writeup of the September 2010 GMOD Meeting. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project. *Registration: *Registration for the March 2011 GMOD Meeting is $80 on or before February 18 $95 after February 18 Please register early, both to save money, and ensure a spot. You are also strongly encouraged to submit a talk and/or sign up for (or propose) a Satellite Meeting. Details on transportation, suggested lodging, and other logistics are on the GMOD Americas 2011 page. This meeting, and all GMOD Americas 2011 events, are jointly sponsored by NESCent and the Galaxy Project. Hope to see you in North Carolina! Dave Clements Galaxy Project PS: And I hope to see you in the Netherlands as well! *The abstract submission deadline for the Galaxy Community Conference is Feb 28.* See http://galaxy.psu.edu/gcc2011/Abstracts.html -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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python2.6 UserWarning: Unbuilt egg for pytz
by Vipin TS 11 Feb '11

11 Feb '11

Hi all, Last day we upgraded our galaxy service computing cluster nodes operating system from Ubuntu hadry to lucid 10.4. We updated python eggs and now getting an Warning message, it apparently kills the galaxy jobs. Warning message as follows: /home/abc/galaxy/lib/galaxy/eggs/__init__.py:332: UserWarning: Unbuilt egg for pytz [unknown version] (/usr/lib/python2.6/dist-packages) env = pkg_resources.Environment( platform=pkg_resources.get_platform() ) >From the warning message I can see that the problem with unbuilt egg for pytz module. Before approaching you I googled the same and got a good thread which explains similar kind of issues ( https://bugs.launchpad.net/ubuntu/+source/distribute/+bug/576434). I followed #9 from TJ and made a work around and unfortunately no luck. Does anyone had a problem with this before, if yes I like to hear from you that how do u managed to get rid of the warning message. Many thanks, Vipin T S Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany

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New Remote Job Runner
by John Chilton 11 Feb '11

11 Feb '11

Hello, We are looking at integrating some tools into Galaxy for a domain where many of the existing programs are Windows only. My desire is to write tool files and have the certain jobs run remotely on a Windows host (our Galaxy servers are Linux). It wasn't clear how to do this with the existing job runners since they all seem to require a shared file system and absolute file paths that are the same on the Galaxy server as they are on the remote execution hosts. I developed a new job runner that allows for the remote execution of jobs that also rewrites paths and stages files as part of the job execution. There is a server application that needs to be running on the remote machine (*nix or Windows). This application is likely easier to setup/configure than SGE/PBS/etc... because it is a simple Python paste application, with just a few configuration options. There may be valid use cases for this approach for non-Windows applications as well - if you would like a lighter weight server component on the remote system, if shared file systems are impossible/impractical, etc.... The path rewrites are not going to cover every possible way an absolute path can sneak into the execution, so this is only useful for a subset of tools. But it does handle normal file inputs and outputs, config files, and scripts in the tool definition directory. I welcome input/advice on this approach or the implementation. If there is any way I can improve the code base to the point where it can be included in galaxy-central I would be more than happy to make the desired changes. If not, it is out there for people to use if they have a similar use case. The server application as well as a patch to add the runner/client to a galaxy-central installation can be found at: https://bitbucket.org/jmchilton/lwr/src Thanks for your time, John ------------------------------------------------ John Chilton Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 E-Mail: chilton(a)msi.umn.edu

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Send data to GBrowse
by Liisa Koski 11 Feb '11

11 Feb '11

Hi, I have just installed Galaxy and am trying to configure it to allow display of data on my local installation of GBrowse. I have edited tool-data/shared/gbrowse/gbrowse_build_sites.txt (species http://domain.ca/cgi-bin/gbrowse/species species) As well as universe_wsgi.ini (gbrowse_display_sites = species) However I do not see a link in history items after I stop and start the server. Is there something else I'm missing? Thanks in advance for your help, Liisa

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file upload speeds
by Glen Beane 11 Feb '11

11 Feb '11

I've been doing some testing with a Galaxy instance running on my laptop for some tools we are developing. I am uploading a file into Galaxy from a URL to use as test input (~1.5GB tabular) I can download this file to my laptop in ~30 seconds with wget, while if I pull from the same URL into Galaxy it takes about 30 minutes. I set the file type so Galaxy did not have to auto-detect. This seems very slow considering it only takes about 30 seconds to get the file over the network and write it to disk. What is Galaxy doing that makes this file upload so slow? We also tried defining our own datatype (data, not tabular with the thought that maybe Galaxy tried to examine tabular files), but it is still very slow. In production our input files will grow to be much larger than this (although we'll probably abandon tabular for a more compact binary format by then). -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153

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Setting Metadata
by SHAUN WEBB 11 Feb '11

11 Feb '11

I seem to remember there being talk of a parameter you can set in the universe file that allows you to limit the size of files for which metadata is set when galaxy uploads a file. Was this put in to production? Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Installation Issue on Centos/python 2.4
by John Powell (NIH/CIT) [E] 10 Feb '11

10 Feb '11

Trying to install a local copy of Galaxy for evaluation. Downloaded the "stable" version using: hg clone https://bitbucket.org/galaxy/galaxy-dist I am installing it on a Centos 5 x86_64 Linux kernel which has python 2.4.3 installed. When running "sh setup.sh" the installation stops with an error building the "python_daemon" egg. In checking, it is trying to download/build python_daemon 1.5.5 (specified in the eggs.ini). This version of python_daemon uses syntax that depends on python >= 2.5. Your "README" indicates.... Galaxy requires Python 2.4, 2.5 or 2.6. To check your python version, run: ... Does Galaxy still run under python 2.4? (PS: I have lots of Linux/Perl experience, but virtually no python expertise.) Thanks.... -------- //=\ John Powell, CAPT, Ret. USPHS Phone: (301) 496-2963 \=// Building 12A, Room 2033 FAX: (301) 402-2867 //=\ National Institutes of Health \=// Bethesda, MD 20892-5624 Work: jip(a)helix.nih.gov //=\ Personal: jpowell(a)erols.com \=// //=\ BioInformatics & Molecular Analysis Section-BIMAS/CBEL/CIT/NIH -------------------------------------------------------------------------

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Re: [galaxy-dev] [galaxy-user] Galaxy does not startup on machine with no Internet access
by Nate Coraor 10 Feb '11

10 Feb '11

Sonali Amonkar wrote: > Hi, > > > I'm trying to install and run galaxy-dist-8729d2e29b02 on a Linux RHEL 5.5 box. This machine has no direct access to the Internet. I followed the steps listed on the page https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs to download the eggs offline and placed them in the correct location. > > Now when I try to run Galaxy (sh run.sh), it appears to be stuck trying to contact http://128.118.200.71 - this was seen through netstat. > > [workflow@vm-ps4121 galaxy-dist]$ netstat -antp | grep tcp > (Not all processes could be identified, non-owned process info > will not be shown, you would have to be root to see it all.) > tcp 0 1 10.88.176.157:44233 128.118.200.71:80 SYN_SENT 5796/python > > Why does galaxy try to connect to this server when all the eggs are already updated? > > My questions are: > > > 1. Can galaxy-dist-8729d2e29b02 can be run on a box with no Internet access? > > 2. How does one enable this no-Internet-available setting in galaxy-dist-8729d2e29b02? Hi Sonali, There were two bugs which were preventing all of the eggs from being downloaded by the egg packaging script. These are resolved in 5038:559a9ad2844d. This changeset is available in our in-development repository. It will be in the distribution repository at some point within the next few weeks, or you can pull the bleeding edge directly with: % hg pull -u http://bitbucket.org/galaxy/galaxy-central/ --nate > > Thank you for your time. > > Regards, > Sonali Amonkar > > DISCLAIMER > ========== > This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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Fwd: [bioinfo-core] request for speakers: ISMB 2011 Vienna, workshop sessions
by Dave Clements 09 Feb '11

09 Feb '11

Hello all, In addition to the Galaxy organized workshop proposal that I just sent out, there is another workshop proposal being created that may be of interest to anyone working in a sequencing center. See below for details. Their deadline is tomorrow (Thursday) as well. Contact Brent if you have questions. Thanks, Dave C. ---------- Forwarded message ---------- From: Richter, Brent G. <BRICHTER(a)partners.org> Date: Tue, Feb 8, 2011 at 7:59 AM Subject: [bioinfo-core] request for speakers: ISMB 2011 Vienna, workshop sessions To: bioinfo-core(a)lists.open-bio.org Dear bioinfo-core community: Thanks to your feedback, we have identified two broad session topics for the workshop at ISMB 2011 in Vienna July 15 to 19th (roughly). Workshop proposals are due this Friday and we ask for your feedback on the topics and request short speaker proposals if you desire to present within one of the sessions. Please provide proposals by Thursday to myself or one of the co-organizers (Fran Lewitter, Simon Andrews or David Sexton). Topic 1: Analysis Pipelines for NGS--the school of hard knocks. A major goal of the bioinformatics core facility is to deliver high-quality data and tools to the researcher. In NGS workflows, core facilities deliver both default data from analysis pipelines as well as allow investigators to use those pipelines directly. However, there can be major issues in doing so. This topic will explore the pitfalls by focusing on what information is missed by relying on standard pipelines only. How can one actually get it wrong by delivering only the results of a standard pipeline? What is the value of the intermediate data that you may not look at but if you do, there can be some rather interesting finds? Time and value can be in conflict in these situations as in-depth QA/QC of data beyond standard pipelines. Topic2: Management of Core Facilities. We will explore different business models of bioinformatics core facilites and their setup including business models, recharging, funding, staff retention, and performance evaluations and metrics. This is a topic we have discussed throughout the years, but continues to be of high interest. Thanks! Brent 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 the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ bioinfo-core mailing list bioinfo-core(a)lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioinfo-core -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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ISMB/ECCB Workshop Proposal, due Friday, Feb 11
by Dave Clements 09 Feb '11

09 Feb '11

Hello all, The Galaxy Project is putting together a workshop proposal for ISMB/ECCB. The theme of the proposed workshop will be "Genomics for Emerging Models" or "Genomics: Flying without a reference". We want to have 4 talks that show attendees particular solutions to challenges that arise when working with organisms that don't have a closely related reference genome available. *The proposal is due Friday, February 11*, in just two days. Our aim is to highlight the solutions, with Galaxy gluing it all together, but not being the focus of the workshop. We want to highlight the science while also demonstrating the power of Galaxy. If you have an approach that addresses a challenge with non-model organisms (and that approach involves Galaxy!), please consider presenting it at ISMB as part of this workshop proposal. *If we get more than 4 proposals, we'll make a final call on what to include in the proposal on Thursday night. * Workshop guidelines and info are at http://www.iscb.org/ismbeccb2011-submission-details/workshops. Please let me know if you have any questions. Thanks, Dave C -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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galaxy-dev February 2011