- galaxy-dev - lists.galaxyproject.org

Huttenhower Galaxy bug
by Erin McKenney 21 Apr '14

21 Apr '14

Hello, I am trying to use LEfSe (on the Huttenhower Galaxy instance) to analyze the data table attached. I formatted the table according to LEfSe guidelines, but the table cannot be formatted after it is loaded to Galaxy. I also tried formatting a table that was successfully analyzed on the Huttenhower instance a year ago. That (previously successful) table cannot be formatted either. I suspect that there is a bug. Can you please help me to resolve the bug or tell me an alternative way to analyze the data? Thanks, Erin

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GCC2014 Poster Abstracts due April 25, THIS FRIDAY
by Dave Clements 21 Apr '14

21 Apr '14

Hello all, This is just a reminder that poster abstracts for the 2014 Galaxy Community Conference (GCC2014) *are due this Friday. * Abstracts can be submitted at https://wiki.galaxyproject.org/Events/GCC2014/Abstracts Note that posters are reviewed and accepted on a rolling basis, until all slots are full. The deadline is this Friday but sooner may be better. In other news: - We are delighted to have Steven Salzberg as the keynote speaker<https://wiki.galaxyproject.org/Events/GCC2014#Keynote_Speaker> . - Registration for the GCC2014 hackathon<https://wiki.galaxyproject.org/Events/GCC2014/Hackathon>is now open - Early registration<https://wiki.galaxyproject.org/Events/GCC2014/Register>for the GCC2014 Training Day and Meeting<https://wiki.galaxyproject.org/Events/GCC2014/Program>are also open - Abstracts <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>for accepted talks will start showing up on the website this week. Thanks, and hope to see you in Baltimore, Dave C On Fri, Feb 14, 2014 at 1:33 PM, Dave Clements <clements(a)galaxyproject.org>wrote: > Hello all, > > *We are pleased to announce that Early Registration > <https://wiki.galaxyproject.org/Events/GCC2014/Register> and Talk and > Poster Abstract Submission > <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> are now open for > the 2014 Galaxy Community Conference (GCC2014) > <https://wiki.galaxyproject.org/Events/GCC2014>.* > > GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014> will be held at > the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…>of Johns > Hopkins University <http://jhu.edu>, in Baltimore, Maryland<http://visitors.baltimorecity.gov/>, > United States, from June 30 through July 2, 2014. GCC2014<https://wiki.galaxyproject.org/Events/GCC2014>starts with a Training > Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> featuring > four *five* parallel tracks, each with three, two and half hour long > workshops. There are 13 different topics spanning the full Galactic > spectrum of topics. Take a look!<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> > > *Early registration > <https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open. > Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training > Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main > meeting) starting at $140 for post-docs and students. Registration is > capped this year at 250 participants, *and we expect to hit that limit*. > Registering early assures you a place at the conference and also a spot in > the Training Day workshops you want to attend. > > You can also book affordable conference housing at the same time you > register. See the conference Logistics page<https://wiki.galaxyproject.org/Events/GCC2014/Logistics>for details on this and other housing options. > > *Abstract submission > <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral > presentations and posters is also open. Abstract submission for oral > presentations closes April 4, while poster submission closes April 25. > Poster authors will be notified of acceptance status within two weeks of > submission, while presentation authors will be notified no later than May2. > *Please consider presenting your work. If you are dealing with big > biological data, then this meeting wants to hear about your work.* > > The *GigaScience <http://www.gigasciencejournal.com/>* "Galaxy: Data > Intensive and Reproducible Research" series announced for the last > conference has published its first papers<http://www.gigasciencejournal.com/series/Galaxy>, > *and is continuing to take submissions for this year's meeting and beyond*. > BGI is also continuing to cover the article processing charges until the > end of the year, and for more information see their latest update<http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibilit…>. > > > Thanks, and hope to see you in Baltimore! > > The GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers> > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://wiki.galaxyproject.org/ > -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Trackster : Error visualising VCF
by Saket Choudhary 21 Apr '14

21 Apr '14

I am trying to visualise VCF exported from: ftp://ngs.sanger.ac.uk/production/cosmic/CosmicCodingMuts_v68.vcf.gz However I get the following error: (Both on Galaxy Main and Local installation) Input error: Chromosome 1 found in your input file but not in your genome file. needLargeMem: trying to allocate 0 bytes (limit: 100000000000) The input file seems to be conforming to VCF4.1 format. Is this an issue with trackster instead? Saket

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bug_losing_links_box
by Mélanie Hachet 19 Apr '14

19 Apr '14

Hello, I would like to report a bug. I'm using galaxy in local and I was detected this bug 2 months ago. First, several inputs are necessary for a box (tool) in order to create a workflow. Then, the workflow is saved with several links for one box. So I launched the workflow but i can put only one input. When I looked the workflow, only one link is kept (the last one marked), others aren't kept. However the script corresponding to the box run well independently. If you need any further information, feel free to contact me. Best regards. Mélanie Hachet

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Error Downloading Reference Genomes using Manage Local Data ( AttributeError: 'JobManager' object has no attribute 'deferred_job_queue')
by John Lockhart 18 Apr '14

18 Apr '14

I am attempting to set up a local instance of Galaxy for a bioinformatics lab, but have been unable to add reference genomes to the instance due to this error. I've tried redoing the install, but still receive the error. Any solutions or alternative methods of installing genomes to local instances would be very appreciated. Traceback: URL: http://localhost:8080/data_admin/download_build File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 377 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/data_admin.py', line 134 in download_build jobid = trans.app.job_manager.deferred_job_queue.plugins['GenomeTransferPlugin'].create_job( trans, url, dbkey, longname, indexers ) AttributeError: 'JobManager' object has no attribute 'deferred_job_queue'

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Functional Tests and ftype
by Saket Choudhary 18 Apr '14

18 Apr '14

I happened to copy Peter's .travis.yml for running tests for some of my packages. However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908 AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control I am already passing it the correct ftype : https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_… Is there something I am missing? Saket

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User usage stats in local instance
by Alejandro Barrera 18 Apr '14

18 Apr '14

Hi, Apologizes if this is not the right place to ask this sort of questions, but I have been asked to report user usage in our lab’s instance of galaxy. In order to crunch the numbers by user (number of logins per month, number of jobs, memory usage, etc.), I thought that in principle, I could ask that info directly to the database (in our case, a MySQL instance). However, given the complex database schema, it looks like this is not the way to do it (at least, not the easy one...). Does anyone have experience retrieving this information? Many thanks in advance, Alex -- Alejandro Barrera Bioinformatics Developer University of Pennsylvania www.biociphers.org

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Galaxy Hackathon at GCC2014
by Dannon Baker 17 Apr '14

17 Apr '14

Galaxy has a fantastic developer community, from the very active mailing lists and #galaxyproject IRC channel to individuals who have submitted literally hundreds of pull requests and patches. We are always looking for ways to interact with existing community members and get even more people involved. To that end, we’re thrilled to officially announce the very first Galaxy Hackathon (http://bit.ly/gcc2014hack) The hackathon will be a three day event taking place at Johns Hopkins immediately preceding GCC2014 from June 28th-30th. Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or Cloudman!) with other folks? The Galaxy Hackathon will be a great opportunity to meet and work closely with other community and Galaxy Team members over the course of three days, culminating in some really great improvements and new features to show off at the Galaxy Community Conference afterward. Participation in the hackathon itself is completely free, but there's limited space so if you're interested and would like to participate please go ahead and book both your lodging and hackathon seat at http://bit.ly/gcc2014hackreg. To help organize ideas and people into more concrete projects, we've also set up a hackathon-specific Trello board that we'd love for everyone to go ahead and start using at https://trello.com/b/3YgU637b/gcc2014-hackathon. The board is public and open to commentary and voting, but to create new cards you’ll need to be added as a member so please note the instructions on the board for that. Finally, we are very happy to have Curoverse (https://curoverse.com) on board as the exclusive Peta level sponsor of the hackathon. If you know of any other group that might be interested in sponsoring at the Giga level please let us know. We hope to see you in June, and can't wait to see what we can accomplish! -Dannon Baker on behalf of the GCC2014 Hackathon Organizing Committee

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User usage stats in local instance
by Alejandro Barrera 17 Apr '14

17 Apr '14

Hi, Apologizes if this is not the right place to ask this sort of questions, but I have been asked to report user usage in our lab’s instance of galaxy. In order to crunch the numbers by user (number of logins per month, number of jobs, memory usage, etc.), I thought that in principle, I could ask that info directly to the database (in our case, a MySQL instance). However, given the complex database schema, it looks like this is not the way to do it (at least, not the easy one...). Does anyone have experience retrieving this information? Many thanks in advance, Alex -- Alejandro Barrera Bioinformatics Developer University of Pennsylvania www.biociphers.org

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Re: [galaxy-dev] galaxy-dev Digest, Vol 94, Issue 22
by Dooley, Damion 17 Apr '14

17 Apr '14

Thanks for your input, John. I see, so from what you say, anything installed via pip in the virtual environment then exists in the module/class include namespace within galaxy python command line tool code. Good to know. I'll note that this approach is compatible with toolshed tools (I'm testing it via one) because it relies on a galaxy admin managed .loc file to list the generic and customized reporting modules. The (toolshed) reporting tool ships with a .loc file that doesn't reference any customized reports, e.g. blast_reporting_templates.loc.sample is #value name description # Add list of html templates here templates.html_report Standard Report Provides report with sections and table sections And then a galaxy admin adds an entry: # Customized templates listed below templates_custom.html_report Customized report Test customized report Task for getting a customized report in place does require manual steps though: customized module, addition of the .pth file, and editing of the above .loc file. Damion ------------------------------ Message: 4 Date: Wed, 16 Apr 2014 06:47:14 -0500 From: John Chilton <jmchilton(a)gmail.com> To: "Dooley, Damion" <Damion.Dooley(a)bccdc.ca> Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> Subject: Re: [galaxy-dev] Can a tool upload a .loc file that is then ... RENAME: custom galaxy tool python modules Message-ID: <CANwbokfAJCLWH7afNk-s7yZXKcz6pWYVq4Ttn0Q=ueZVFXtHtg(a)mail.gmail.com> Content-Type: text/plain; charset=UTF-8 If this is working it sounds reasonable. I think my approach might be to setup Galaxy inside a virtualenv (as recommended here https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer) and just install your extra dependencies inside that virtualenv using pip. $ . <path_to_virtualenv>/bin/activate $ pip install dependency1 $ pip install dependency2 ... After that you should be able to just do a normal Python import. I think you have another open question about the next steps of this - but just to make it explicit - everything is going to work better in "the Galaxy ecosystem" if you can avoid calling code from tools like this and just use the sort of stock options. For instance - neither of these approaches will work with the tool shed. Sometimes that is not possible - I understand that - but I just thought I would put the disclaimer out there. -John

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