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

makeblastdb wrapper
by Espin, Almudena 09 Nov '12

09 Nov '12

Hi guys, I am writing a wrapper for makeblastdb. The problem is that Galaxy doesn’t support the blastdb data format, so this has to be added if a makeblastdb wrapper is to work properly. I have problems modifying the registry.py, Could anyone specify which changes have to be done? Thank you

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Jobs are slow to start on my galaxy instance. Used to be much faster
by Anthonius deBoer 07 Nov '12

07 Nov '12

Hi, Jobs that I start on my in-house Galaxy instance now take up to 3-4 min to go from queued to Running, even though there is nothing much going on on the galaxy server... I have been running this instance since June and use a relatively new version of Galaxy-central (Last update, 22-Aug changeset: 7535:bf6517b2b336) I have noticed that my jobs table in the galaxy Postgres database contains about 60,000 jobs... Could that be the culprit? Does it slow to the complete database to see if there are any jobs that need to run? Could I purge the jobs and related tables to speed up the submissions? Thanks, Thon

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MrBayes wrapper - set parameters through Galaxy?
by Gomez, Ann 06 Nov '12

06 Nov '12

Hello all, I've written a MrBayes wrapper that accepts a Nexus file (presumably containing a data block and a command block). In order to make it a bit easier for new users, I was hoping to be able to let users specify some parameters, such as their model, in Galaxy, as opposed to including it in the command block of the Nexus file. Am I correct in thinking this is not possible since MrBayes does not have a way to invoke commands in-line? To clarify for non-MrBayes people, my limited understanding is that you either invoke the interpreter with "$ mb" and then enter your commands, or directly execute a Nexus file (containing the data and commands) with " $ mb <nexusfilename>". Please correct me if I'm missing something or thinking about this completely wrong. I'd appreciate any input about MrBayes or a similar kind of tool. Cheers, Ann Ann Gomez Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada KW Neatby Bldg | éd. KW Neatby 960 Carling Ave| 960, avenue Carling Ottawa, ON | Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel: ann.gomez(a)agr.gc.ca <mailto:ann.gomez@agr.gc.ca> Telephone | Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government of Canada | Gouvernement du Canada

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Unnamed histories proliferating, can't get to my data
by Karger, Amir 05 Nov '12

05 Nov '12

I'm using Galaxy from June, 2012. (Sorry if there's already a fix.) We've got it "working" in production. We've gotten whole pipelines to run. However, we occasionally get situations where we upload file (using the FTP mechanism), which seems to be fine, but then I can't get to the data. I went to Saved Histories, and selected Switch, and it outlined the line in blue and wrote "current history" next to it. But the right pane still shows "Unnamed history" with no data in it. Then if I go back to Saved Histories, I get one or two new Unnamed histories, created within the last few minutes. I just tried to "View" the history, which worked (in the middle pane) and clicked "import and start using history". This seemed to work, but I got three panes inside the middle pane! When I go back (again) to saved histories, there are 3 histories - one the imported one with 2 steps, two unnamed histories, all created < 1 minute ago. We just asked a beta tester to play with things, and he uploaded two fastqs, but had what sounds like a similar problem. Any thoughts on what's happening? Thanks, -Amir Karger Research Computing Harvard Medical School

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phylotastic hackathon (Jan 28 - Feb 1, Tucson, AZ) of possible interest to galaxy developers
by Arlin Stoltzfus 05 Nov '12

05 Nov '12

Dear galaxy developers-- I'd like to bring your attention to the call for participation included below this message. A "Phylotastic" system is a distributed tree-of-life delivery system composed of web services. Although it is not readily apparent from the presentation linked below, the project includes some work on using Galaxy as a framework for managing a phylotastic workflow. See the demos page (http://phylotastic.org/demos.html) and the "Making Galaxy Phylotastic!" screencast (http://youtu.be/kMME658xOu4 for more. I would be happy to respond to questions about the project. Please consider applying if you are excited by the project and think that you can contribute. Regards, Arlin ----- Phylogenies! Hacking! Tucson in January! An implicit promise of the Tree of Life project is that, ultimately, expert knowledge of species phylogeny will be accessible and usable by everybody. In other words, we will all be able to get the species trees we need, in a useable form, when we need them. The Phylotastic project aims to make that vision a reality, by developing a loosely coupled system of components that, in response to a user’s query (a list of taxa plus conditions), will rectify names, find suitable source trees, prune and graft to get the right species, estimate branch lengths, and return the results with metadata on sources and methods. In June 2012, the HIP (Hackathons, Interoperability, Phylogenies) working group of NESCent staged a hackathon (http://en.wikipedia.org/wiki/Hackathon) to prototype components of a Phylotastic system, and implement demos to show their potential. Thanks to 25 participants who responded to an open call (just like this one), that hackathon was an extraordinary success (see http://phylotastic.org/) Now we are gearing up for a second hackathon, to take another step toward providing computable, convenient, credible access to the Tree of Life. We aim to recruit a diverse group of participants, including students, faculty, postdocs, and staff of both genders and from different backgrounds. Only some of the seats at the hackathon will be filled by expert hackers who spend their time coding. We also need folks who can: * Provide knowledge of workflows and downstream uses of trees * Design user interfaces * Test software * Make screencasts, develop tutorials, and document user experiences Applications are now being accepted to Phylotastic 2, which will take place January 28th, 2013 to February 1st, 2013 at the BIO5 facility in warm and sunny Tucson, AZ (http://bio5.arizona.edu/about-bio5) Information on how to apply is provided below. Partial support (and, if funds allow, full support) for travel, food and lodging will be available to each successful applicant who indicates need. We particularly welcome applications from women and members of underrepresented groups. To understand how you might be able to contribute, review the slideshow (ppt format, http://bit.ly/RWRgIc, or PDF format, http://bit.ly/POaoci) consult the web site (phylotastic.org) or contact a member of the HIP leadership team (listed below). Sincerely, the HIP (Hackathons, Interoperability and Phylogenies) Leadership Team HOW TO APPLY Before 16 November, 2012 at midnight, EST, fill out the online form here http://tinyurl.com/PhyloTastic2. Note that: * The application form asks you to describe how you can contribute to Phylotastic. Remember that we are not just looking for expert coders. There are many other ways to contribute. * Support for travel, housing and meals will be available to each successful applicant who indicates need. * Please understand that your application is not a guarantee of participation in the event. Funds and space are limited: we may not be able to sponsor every individual who is qualified to participate. LEADERSHIP TEAM Karen Cranston, karen.cranston(a)nescent.org Brian Sidlauskas, brian.sidlauskas(a)oregonstate.edu Arlin Stoltzfus, arlin(a)umd.edu Mike Rosenberg mrosenb(a)asu.edu Brian O’Meara, bomeara(a)utk.edu Mark Westneat mwestneat(a)fieldmuseum.org Enrico Pontelli epontell(a)cs.nmsu.edu Rutger Vos rutgeraldo(a)gmail.com Naim Matasci nmatasci(a)iplantcollaborative.org ------- Arlin Stoltzfus (arlin(a)umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD, 20850 tel: 240 314 6208; web: www.molevol.org

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Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch
by Sascha Kastens 03 Nov '12

03 Nov '12

Hi Dev-Team, are you planning or maybe working on an update which enables the possiblilty to run workflows in batch mode with paired end data? Cheers, Sascha

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JBrowse direct export to Galaxy
by Erik Derohanian 01 Nov '12

01 Nov '12

Hello, I am a JBrowse Dev hoping to add the ability to export data directly from JBrowse (JavaScript) to Galaxy (without exporting from JBrowse, saving locally, opening Galaxy, loading file from drive). I have looked through the wiki page on Data Sources<http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources>, but JBrowse is client-side only. I was wondering if anybody knew of a different way to do this, or had any pointers. Thanks, Erik Derohanian

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Re: [galaxy-dev] Empty TopHat output
by Joachim Jacob 01 Nov '12

01 Nov '12

The same here. Cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Parallelism tag and job splitter
by Edward Hills 01 Nov '12

01 Nov '12

Hi Galaxy-Team, After reading a message on this mailing list about the job splitter I began to investigate what and how this is used. Unfortunately I have been unable to find any documentation on your website for it. Am I blind and missing it or is it yet to be properly documented? Sorry if this turns to be out a pointless exercise, but it would be extremely useful for my Galaxy development. Cheers, Ed

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Join version 1.0.0 error
by Scooter Willis 31 Oct '12

31 Oct '12

Using large amazon instance Trying to do an interval join of SNPs as output from pileup 120,000 regions(5.5Mb) with with snp135Common 12,000,000(425Mb) and get the following errors. The goal is to pickup rs id's for known SNPs in the list of SNPs. Is this a memory issue? I was able to do the operation against chr1 as a test. Thought about chaining the outputs and doing against a file for each chromosome to make smaller files but then I have a mess where rs id's are in different columns. 71: Join on data 38 and data 36 0 bytes An error occurred running this job: /opt/sge/default/spool/execd/ip-10-191-53-90/job_scripts/14: line 13: 5517 Killed python /mnt/galaxyTools/galaxy-central/tools/new_operations/gops_join.py /mnt/galaxyData/files/000/dataset_75.dat /mnt/galaxyData/files/000/dataset_77.dat

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