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

Tags API
by Kyle Ellrott 12 Nov '12

12 Nov '12

Are there any docs or examples about how to add/remove tags from items via the galaxy web-api? Thanks, Kyle Ellrott

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workflow not working
by Rolando Mantilla 12 Nov '12

12 Nov '12

hello guys I'm kinda new using galaxy but I'm having an issue I tried to run my workflow and it just stopped, I was able to load both of the sequences but I could not run the whole workflow. I do have enable_job_execution=True, so I don't know what is wrong, please help!!

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galaxy/cloudman failure handling
by Jorrit Boekel 12 Nov '12

12 Nov '12

Dear list, I would like to start using Amazon's spot pricing model for my Galaxy/Cloudman instances (e.g. an on demand master node with spot instance worker nodes). However, this means that Amazon at times of spot prices higher than my set price limit will shutdown my instances without notion. I was therefore looking for fault tolerance mechanisms in the galaxy project, which I seem to remember existed. Somehow I can't find anything about it right now though. I've tested a little bit, and it seems that as soon as one reboots instances or manually kills a job or task, the whole job is deleted and set to error state. I am not that knowledgeable in cluster computing, so I don't really know what handles what here, but this would be an ideal starting point to learn something about SGE and queue handling. Is there any mechanism in place that deals with node failure, network problems, etc? If not, would it be hard to implement? cheers, jorrit boekel

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Phylotastic hackathon #2 -- last call for applications (due by Friday, 16 Nov, midnight EST)
by Arlin Stoltzfus 12 Nov '12

12 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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Bug report : JSONDecodeError
by Mathieu Bahin 12 Nov '12

12 Nov '12

Hi, I am using my own Galaxy instance and I had a problem removing a tool from the tool shed : mothur. The installation was ok and I the mothur tool running without any problem. But when I tried to uninstall the tool, I get an error (screenshot enclosed). And I get the same every time I try to go on the 'Manage tool shed repositories' in the Admin panel. I have tried to rebuilt the eggs and to restart Galaxy basically. Actually, I don't really understand the error message. Cheers, Mathieu Bahin

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Error: change attributes generates error on fresh dist-release
by Bossers, Alex 12 Nov '12

12 Nov '12

Hi All, Due to previous DB errors we decided to let galaxy-dist repopulate the database (MySQL). We purged all tables from the DB and when restarting galaxy it repopulates the DB on the fly while doing all migration steps. A nicely running galaxy as the result. I encountered a strange error which might be linked to this... or not... When changing the attribute of a dataset I get the error below; We never had this before so my guess is that the DB is not constructed properly. We are at tip 7986:12fcd068b12e of the dist release. Any pointer to fix this? There is currently no user-data or histories anymore so I can experiment... before I open it for running publicly again... Thanks; Alex URL: http://galaxy.wur.nl:8080/galaxy/datasets/b4bd1d7d8ca50a82/edit Module paste.exceptions.errormiddleware:143 in __call__ >> <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> environ, self.app) Module paste.wsgilib:539 in intercept_output >> <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:496 in edit >> <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> all_roles = trans.app.security_agent.get_legitimate_roles( trans, data.dataset, 'root' ) Module galaxy.security:192 in get_legitimate_roles >> <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.get_all_roles( trans, cntrller ) Module galaxy.security:168 in get_all_roles >> <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> return self.sort_by_attr( [ role for role in roles ], 'name' ) Module galaxy.security:137 in sort_by_attr >> <http://galaxy.wur.nl:8086/galaxy/datasets/b4bd1d7d8ca50a9f/edit> intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq ) AttributeError: 'NoneType' object has no attribute 'name'

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Where is the xml file of "edit attribute"? and history name
by julie dubois 12 Nov '12

12 Nov '12

Hi, I've redirected all of my outputs in an other directory with my own names after each run of tools.. But when the users want to rename their datasets on the history, I would want that this change occurs on my output files already register in the computer. So where can I find the xml file of the function "edit attribute" and from this file, can I take the real name of my output file before the change? Another question is about the history name : because the users use several history, I need to know how call the variable of the history name ; for exemple if an output variable is $output, the history name of this variable is : $output.history_name ? or $output.history.name? or if this name is not accessible in this way, may be the history id ? In my first step when I rename an output, I take the $output.hid which indicate me the number of the dataset in an history. But I've not found the name of this history. Thanks Julie

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How to get a compressed output in the history
by Philipe Moncuquet 11 Nov '12

11 Nov '12

Hi dev, I have written a perl script to perform some complex demultiplexing of reads. It works well on my computer but the integration to Galaxy is a bit tricky since it's the first time for me. At one point my perl script generates a bunch of fasta files, I want all this fasta files to be compressed and I use a tar command within the script to do so. I am not sure how to do the same within the Galaxy execution. I think it might work out with the "from_work_dir" attributes of the output tag but I don't know exactly where my script should write these fasta files and compress them so that the archive could be retrieve. I don't know either what to put in the "format" attributes since gz is not in the supported datatype or is it ? Should I create a new datatype ? The ending point of my tool would be to have the user be able to download one compressed file that would contains all the sorted fasta files. Cheers, Philippe

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Uploading files onto local server
by John Clayton 09 Nov '12

09 Nov '12

Dear Sir or Madam, I am having difficult loading files onto my local galaxy instance. I have given myself admin status, but when I attempt to add files to a new library, I get the following message: Error attempting to display contents of library (New data library): (OperationalError) no such column: True u'SELECT dataset_permissions.id AS dataset_permissions_id, dataset_permissions.create_time AS dataset_permissions_create_time, dataset_permissions.update_time AS dataset_permissions_update_time, dataset_permissions.action AS dataset_permissions_action, dataset_permissions.dataset_id AS dataset_permissions_dataset_id, dataset_permissions.role_id AS dataset_permissions_role_id XnFROM dataset_permissions XnWHERE True AND dataset_permissions.action = ?' ['access']. I have tried toggling some things in the universe_wsgi.ini as well as changing the permissions associated with the library. But I still get this message. After looking around a bit on the help site, I cam across the following exchange on one of your boards: http://dev.list.galaxyproject.org/Error-while-uploading-data-from-local-dir… This is a bug that is fixed in revision ecd131b. Sorry for the inconvenience. -- jt However, I have updated to the most recent release using mercurial, so I don't know if this applies to me or not. How can I determine if I have revision ecd131b? I'm running Max Os 10.7 and using Safari to interface with galaxy. Actually, I was using Firefox at first, but it was hanging during file uploads and the problem disappeared when I switched to Safari. I guess this is a separate issue, but has anyone reported similar problems? -- John R. Clayton, PhD Université de Strasbourg Anopheles Group, CNRS UPR-9022 "Réponse Immunitaire et Développement chez les Insectes" Institut de Biologie Moléculaire et Cellulaire (IBMC) 15, rue René Descartes F-67084 CEDEX Strasbourg France Tel: +33 3.88.41.70.96 Fax: +33 3.88.60.69.22 Email: j.clayton(a)ibmc-cnrs.unistra.fr http://www-ibmc.u-strasbg.fr/ridi/index.php?cont_id=9&lang=en

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Account had be deleted ?
by Diam Hsu 09 Nov '12

09 Nov '12

Dear Sir or Madam, I used to use Galaxy to analyze NGS data, but these two days I could't login my Galaxy account, it also told me that my account has been marked deleted, and asked me to contact the Galaxy administrator to restore my account. Could you help me restore my accounts because I have to use Galaxy to finish my thesis. Thank you very much for your help!!! Best regards, Dima Hsu Graduate student, Graduate Institute of Biomedical Informatics Taipei Medical University, Taipei, Taiwan Email:b1984073@gmail.com

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