- galaxy-dev - lists.galaxyproject.org

Docker tools
by Abdulrahman Azab 02 Mar '16

02 Mar '16

Hi Galaxy, I'm working on a project for running galaxy on the top of a docker swarm cluster. The docker tag in the tool xml so far supports access only to the local docker host. To submit to the swarm manager, the command should be: $ docker -H tcp://<manager-ip>:<manager-port> run ... instead of: $ docker run ... Is it possible to add an xml tag attribute to support that option? This would off course require that all files are located in a shared file-system. Thank you, Yours sincerely, Abdulrahman Azab Head engineer ELIXIR.NO, Genomic Hyperbrowser Team Research Group for Biomedical Informatics, Department of Informatics (IFI) Research Support Services Group, University Center for Information Technology (USIT) University of Oslo, Boks 1072 Blindern, NO-0316 OSLO, Norway Email: azab(a)ifi.uio.no, azab(a)usit.uio.no Cell-phone: +47 46797339 ---- Senior Lecturer in Computer Engineering Faculty of Engineering, University of Mansoura, 35516-Mansoura, Egypt Email: abdulrahman.azab(a)mans.edu.eg<https://mail.uio.no/owa/abdulrahman.azab@mans.edu.eg>

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Fwd: BOSC 2016 Call for Abstracts
by Peter Cock 02 Mar '16

02 Mar '16

Dear all, As BOSC co-chair I would like to encourage you all to think about attending BOSC 2016, and if you are working on your own open source software for bioinformatics please consider submitting an abstract. See the email below and: http://news.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/ We've had lots of Galaxy related talks at BOSC over the years, and look forward to more abstract submissions from the Galaxy community this year as well. Also, as a member of the Open Bioinformatics Foundation (OBF) Board of Directors, I am delighted to let you know about the new OBF Travel Fellowship which could be used to attend BOSC, or the Galaxy Community Conference (GCC2016) if your work fits: http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/ Thank you, Peter [Galaxy contributor & tool developer, BOSC co-chair, OBF Secretary, etc.] P.S. In case you missed the earlier announcement last year, we finally got rid of the paper forms for OBF membership, see: http://news.open-bio.org/2015/12/10/online-membership-form/ ---------- Forwarded message ---------- From: Peter Cock <p.j.a.cock(a)googlemail.com> Date: Tue, Mar 1, 2016 at 5:56 PM Subject: BOSC 2016 Call for Abstracts To: bosc-announce(a)lists.open-bio.org Cc: bosc-reviewers(a)lists.open-bio.org, "bosc(a)open-bio.org" <bosc(a)open-bio.org> Call for Abstracts for the 17th Annual Bioinformatics Open Source Conference (BOSC 2016), a Special Interest Group (SIG) of ISMB 2016. Dates: July 8-9, 2016 Location: Orlando, FL Web site: http://www.open-bio.org/wiki/BOSC_2016 Email: bosc(a)open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Twitter: @OBF_BOSC and @OBF_News Important Dates: * Call for one-page abstracts opens: March 1, 2016 * Abstract submission deadline: April 1, 2016 * Travel fellowship application deadline: April 15, 2016 * Authors notified: May 6, 2016 * Codefest 2016: July 6-7, 2016, Orlando, FL (confirming venue) * BOSC 2016: July 8-9, 2016, Orlando, FL * ISMB 2016: July 8-12, 2016, Orlando, FL The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual ISMB conference. It is organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results and software. We welcome one-page abstracts on any topic of relevance to open source bioinformatics and open science. Presentation formats are lightning talks, longer talks, and/or posters. We plan to offer a limited number of travel fellowships to help offset expenses for some accepted speakers who would not otherwise be able to attend BOSC – please see the OBF Travel Fellowship announcement for more information: http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/ Session topics include: * Open Science and Reproducible Research * Standards and Interoperability * Data Science * Visualization * Translational Bioinformatics * Bioinformatics Open Source Libraries and Projects If your company or organization is interested in helping to sponsor BOSC 2016, please contact us! Sponsors in 2015 included Google, GigaScience, Curoverse and Bina – we thank them for their support. Please see http://www.open-bio.org/wiki/BOSC_Abstract_Submission for abstract submission instructions, Thank you, BOSC 2016 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Brad Chapman, Christopher Fields, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres, Heather Wiencko

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Galaxy External Authentication and API access
by Lance Parsons 02 Mar '16

02 Mar '16

I am currently using Apache and CAS (https://en.wikipedia.org/wiki/Central_Authentication_Service) to provide external authentication to Galaxy. I'd like to start using the API, however, I've not been able to find a way to get that to work. A while back, someone suggested using the following: <Location "/api"> Satisfy Any Allow from all </Location> However, this breaks the history view at least, since the ajax call is an /api call and no HTTP_REMOTE_USER gets set. Does anyone have any suggestions? I'd love to get this going with some simple configuration... I know I could move over to LDAP, but that is not desirable since it's less secure than CAS. Another option would be to implement CAS within Galaxy, but that does seem like a good bit of work, but perhaps someone is already working on it or at least interested? -- Lance Parsons - Scientific Programmer Carl C. Icahn Laboratory - Room 141 (Temporary) Lewis-Sigler Institute for Integrative Genomics Princeton University

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Alternative methods for external authentication
by Amelia Ireland 01 Mar '16

01 Mar '16

I'd like to set up a galaxy instance to use a custom external authentication system. The documentation has examples of using LDAP and Apache-based authentication, but I wondered if there was a more general method for hooking up a login system. Thanks! Amelia Ireland Integrated Microbial Genomics

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Missing modules after upgrade to 16.01
by C. Ch. 01 Mar '16

01 Mar '16

Hi, I've upgraded to 16.01 and have error messages indicating missing modules. This produces problems while setting the metadata. The processes run, the results are there but the history entry is in red. How can I trigger the installation of all the modules that galaxy needs with the new pip based mechanism? Thanks for the help!Cristian

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Python 2.6 Support
by Dannon Baker 01 Mar '16

01 Mar '16

We're currently discussing when we should stop supporting Python2.6 and it'd be useful to know how much this might impact local Galaxy administrators. Does anyone on the list have strong feelings or concerns about this and want to weigh in? Here's the issue on GitHub for more information and discussion: https://github.com/galaxyproject/galaxy/issues/1596 Thanks! Dannon

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March 2016 Galaxy News: GCC2016 deadlines this month, GSOC 2016, RAD-Seq Hack …
by Dave Clements 01 Mar '16

01 Mar '16

Hello all, The *March 2016 Galactic News <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03>* is hot off the presses: - *GCC2016 <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#GCC2016>* news: - *Oral presentation abstracts due March 20 <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#GCC2016_Abstract_Submi…>.* If you are doing work in data-intensive biology then you are strongly encourage to present your work at the conference. Oral presentations, poster presentations, and the new Visualization Showcase & Software Demos are all opportunities to share your work. - Register early <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#GCC2016_Early_Registra…> and save up to 40% off regular registration costs. Early bird prices start at less than $45 / day for post-docs and students. - Apply for a GCC2016 Scholarship <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Scholarships:_Internat…> . *Applications from international applicants are due March 20.* - The 2016 GMOD Meeting <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#GMOD_Meeting.2C_June_3…> will be held immediately following GCC2016, also at Indiana University. - And, we have a returning sponsor: Please welcome *BioTeam <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Sponsors>* to GCC2016. - *March 7-8: Online IUC Contribution Fest - RADSeq Tools and Workflows <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#March_7-8:_Online_IUC_…>* - *Galaxy in Google Summer of Code <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Galaxy_in_Google_Summe…>* - Twelve other upcoming events <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Upcoming_Events> - 54 new publications, including 4 highlighted pubs <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#New_Papers> - New jobs <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Who.27s_Hiring> - New releases <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Releases>, including the new CloudBridge <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#CloudBridge_0.1.0> and two important security announcements <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#Security_Announcements> - Two new Galaxy servers <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#New_Public_Galaxy_Serv…> - New ToolShed Contributions <https://wiki.galaxyproject.org/GalaxyUpdates/2016_03#ToolShed_Contributions> Dave Clements and the Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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tmp directory
by Raphenya, Amogelang 01 Mar '16

01 Mar '16

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GATK problems with data manager
by Scott Szakonyi 01 Mar '16

01 Mar '16

Hi all, Sorry to be repetitive, but this issue is really blocking our efforts to develop the workflow that we need in our instance of Galaxy. If anyone has any familiarity with the issue described below, please let me know. I really need to get this solved. One of my co-administrators is having some issues with data indexed/processed with data managers in GATK. His email to me: Currently there is no way to load a genome into versions of GATK above version 1.4. No version seems to be able to load a reference from history and only version 1.4 seems to work with the available picard-gatk data manager. We need to be able to work with these later versions of GATK, 3.4 on the Galaxy tool shed is the latest. Thanks! Scott -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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novoalign in Galaxy
by Peter van Heusden 01 Mar '16

01 Mar '16

Hi there We're busy integrating novoalign in our local Galaxy - there doesn't seem to be a tool around for this, but I recall some people saying they were using (single threaded) novoalign with Galaxy. Does anyone know if tool XML has already been written? If not, we'll just have to write it. Peter

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