- galaxy-announce - lists.galaxyproject.org

June 3, 2013 Galaxy Distribution
by Jennifer Jackson 04 Jun '13

04 Jun '13

June 3, 2013 Galaxy Distribution <http://wiki.galaxyproject.org/News/2013_06_03_Galaxy_Distribution> *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_03>* *Highlights:* * Visualization tool updates to Scatterplot <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Scatterplot> and Trackster <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Trackster>. * Job distribution, error tracking/management, and reporting function improvements to Admin <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Admin> & Core <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Core>. * Multiple Tool <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Tools> updates, History and Dataset <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Histories> upgrades, and other related UI <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#UI> enhancements. * New features and fixes added to the Tool Shed <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Tool_Shed> and related components. * Python 2.5 Support /officially ended/ <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Python_2.5_Support_H…>. * Plus newly merged Pull Requests <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Pull_Requests_Merged> and links to tickets covering key Bug Fixes <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Bug_Fixes>. / http://getgalaxy.org/ /http://bitbucket.org/galaxy/galaxy-dist/ /http://galaxy-dist.readthedocs.org/ // new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable upgrade: $ hg pull $ hg updaterelease_2013.06.03 /Thanks for using Galaxy,/ The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>

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June 2013 Galaxy Update
by Dave Clements 31 May '13

31 May '13

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GCC2013 Early Registration ends this Friday, 24 May
by Dave Clements 20 May '13

20 May '13

Hello all, Early registration <http://bit.ly/GCC2013Reg> for the 2013 Galaxy Community Conference (GCC2013) <http://bit.ly/gcc2013> ends this Friday, 24 May. Early registration saves *up to 75% off regular registration costs*, and is downright affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + main meeting <http://wiki.galaxyproject.org/Events/GCC2013/Program>) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations. GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynote, and lightning talks, all about high-throughput biology and the tools that support it. The conference also includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> with in-depth topic coverage of twelve different topics in 15 sessions across 5 tracks. An early program is available<http://wiki.galaxyproject.org/Events/GCC2013/Program> featuring 25 oral presentations, lightning talks and poster sessions, and the just added Birds-of-a-Feather <http://wiki.galaxyproject.org/Events/GCC2013/BoF> gatherings. If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then this conference is for you. Thanks, GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> ! -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Duplicate Accounts on Main
by Dave Clements 17 May '13

17 May '13

Hello all, The terms of use <https://main.g2.bx.psu.edu/static/terms.html> for the Galaxy Project's free Galaxy server, http://usegalaxy.org (a.k.a. Main<http://wiki.galaxyproject.org/Main>) specify Your access to the Service is provided under the condition that you abide by any published quotas on data storage, job submissions, or any other limitations placed on the public Service. *Attempts to subvert these limits by creating multiple accounts or through any other method may result in termination of all associated accounts.* In the past we have dealt with multiple accounts on an ad-hoc basis. Moving forward we are using an automated system to detect, disable, and eventually delete duplicate accounts. If the automated system determines that your account is a duplicate, your account will be disabled and you will receive an email asking you if this is the account you wish to keep. If it is, please follow the directions in the email and your access to that account will be restored. If your account is suspended and you believe that you are not in violation of Main's terms of use, then please contact terms_and_conditions(a)galaxyproject.org. Thanks, The Galaxy Team -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Next GalaxyAdmins Meetup: May 15; Galaxy @ Pathogen Portal
by Dave Clements 14 May '13

14 May '13

Hello all, The next meeting<http://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_05_15> of the GalaxyAdmins Group<http://wiki.galaxyproject.org/Community/GalaxyAdmins> will be held on May 15, 2013, at 10 AM Central US time<http://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_05_15> . Andrew Warren of the Cyberinfrastructure Division<http://www.vbi.vt.edu/faculty/group_overview/Cyberinfrastructure_Division> of the Virginia Bioinformatics Institute <https://www.vbi.vt.edu/> at Virginia Tech will talk about their Galaxy deployment<http://rnaseq.pathogenportal.org/> at Pathogen Portal <http://pathogenportal.org/>, a highly customized Galaxy installation, and also about the group's objectives and future plans. Dannon Baker <http://wiki.galaxyproject.org/DannonBaker> will bring the group up to speed on what's happening in the Galaxy project. Date May 15, 2013 Time 10 am Central US Time (-5 GMT) Presentations *Galaxy <http://rnaseq.pathogenportal.org/> at Pathogen Portal<http://pathogenportal.org/> * Andrew Warren, Virginia Bioinformatics Institute <https://www.vbi.vt.edu/>, Virginia Tech *Galaxy Project Update* Dannon Baker <http://wiki.galaxyproject.org/DannonBaker> Links Meetup Link<https://globalcampus.uiowa.edu/join_meeting.html?meetingId=1262346908659> Add to calendar<https://globalcampus.uiowa.edu/build_calendar.event?meetingId=1262346908659> We use the Blackboard Collaborate Web Conferencing system<http://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/WebinarTech> for the meetup. Downloading the required applets in advance and using a headphone with microphone to prevent audio feedback during the call is recommended. GalaxyAdmins <http://wiki.galaxyproject.org/Community/GalaxyAdmins> is a discussion group for Galaxy community members who are responsible for large Galaxy installations. Thanks, Dave Clements -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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May 2013 Galaxy Update
by Dave Clements 06 May '13

06 May '13

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Fwd: [Gmod-announce] 2013 GMOD Summer School: Apply now!
by Dave Clements 17 Apr '13

17 Apr '13

Hello all, The 2013 GMOD Summer School is now accepting applications. Galaxy will again be included in the topics covered. And Amelia says: Applications are competitive, so we encourage you to apply well before the > deadline, June 10th. So, if you are interested, act soon. Dave C ---------- Forwarded message ---------- From: Amelia Ireland <amelia.ireland(a)gmod.org> Date: Wed, Apr 17, 2013 at 11:15 AM Subject: [Gmod-announce] 2013 GMOD Summer School: Apply now! To: gmod-announce <gmod-announce(a)lists.sourceforge.net>, gmod-devel(a)lists.sourceforge.net We are now accepting applications for the 2013 GMOD Summer School, to be held NESCent, Durham, North Carolina from July 19th to 23rd. The GMOD Summer School is the best way to learn how to install, configure, and use popular GMOD tools, including GBrowse, JBrowse, Galaxy, MAKER, Tripal, WebApollo, and Chado; courses are taught by the tool developers, and there will be evening sessions for those who want to work on their own data or troubleshoot issues with the developers. More information and online application form: http://gmod.org/wiki/2013_GMOD_Summer_School Applications are competitive, so we encourage you to apply well before the deadline, June 10th. If you have any questions, please contact help(a)gmod.org and we will be happy to answer them. -- Amelia Ireland GMOD Community Support http://gmod.org || @gmodproject ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ Gmod-announce mailing list Gmod-announce(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gmod-announce -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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GCC2013 Talk Abstract Submission closes this Friday
by Dave Clements 09 Apr '13

09 Apr '13

Hello all, This is a final reminder that the *deadline for submitting an oral presentation abstract is this 12 April, this Friday*. See http://wiki.galaxyproject.org/Events/GCC2013/Abstracts The poster presentation abstract deadline is 3 May. And in case you missed the announcement about GIgaScience and GCC2013 talks: We are pleased to announce that talks presented at the 2013 Galaxy Community conference will be eligible for consideration to be published in the journal *GigaScience <http://www.gigasciencejournal.com/>* and that BGI<http://www.genomics.cn/en/index>will generously cover the article processing fees for these articles. See the announcement <http://wiki.galaxyproject.org/News/GigaScienceGalaxyCFP>for details. Thanks, Dave C On Mon, Feb 25, 2013 at 3:40 AM, Dave Clements <clements(a)galaxyproject.org>wrote: > Dear Galaxy Community, > > We are pleased to announce that early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > and paper and poster abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> are > now open for the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> > . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University > of Oslo <http://uio.no/>. > > GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity > to participate in two full days of presentations, discussions, poster > sessions, keynotes, lightning talks and breakouts, all about > high-throughput biology and the tools that support it. The conference also > includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> for > the second year in a row, this year with more in-depth topic coverage, more > concurrent sessions, and more topics. > > If you are a biologist or bioinformatician performing or enabling > high-throughput biological research, then please consider attending. > GCC2013 is aimed at: > > - Bioinformatics tool developers and data providers > - Workflow developers and power bioinformatics users > - Sequencing and Bioinformatics core staff > - Data archival and analysis reproducibility specialists > > *Early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > * *saves up to 75% off regular registration costs,* and is very > affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + > main meeting) starting at ~ €95 for post-docs and students. Registering > early also assures you a spot in the Training Day workshops you want to > attend. Once a Training Day session becomes full, it will be closed to new > registrations. Early registration closes 24 May. > > *Abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> > * for oral presentations closes 12 April, and for posters on 3 May. > Please consider presenting your work. If you are working with big > biological data, then the people at this meeting want to hear about your > work. > > Thanks, and hope to see you in Oslo! > > The GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> > > PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> > ! > -- > http://galaxyproject.org/GCC2013 > <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://wiki.galaxyproject.org/ > -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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April 8, 2013 Galaxy Security Release
by Nate Coraor 08 Apr '13

08 Apr '13

A security vulnerability was recently discovered that would allow a malicious person to delete the contents of a history that does not belong to them. The vulnerability was in a method designed to allow users to switch between histories as a convenience from certain messages and is not used for most normal history switching operations. A fix has been provided in the stable branch of the Galaxy distribution and tagged as security_2013.04.08. Administrators are strongly encouraged to upgrade to at least the listed tag or to implement one of the provided workarounds. This changeset *is not* included in the most recent (April 1, 2013) stable release. To upgrade: % hg pull % hg update security_2013.04.08 For Galaxy installations on relatively old versions that administrators are not yet ready to upgrade, there are two workarounds. First, the patch can be downloaded and applied manually: % wget -o history.patch https://bitbucket.org/galaxy/galaxy-central/commits/883216b2eaf2ff05b7771f4… and then: % hg patch history.patch or: % patch -p1 < history.patch In this case, the Galaxy server process(es) must be restarted for the change to take effect. Second, access to this method via the upstream proxy server can be denied. Note that anyone with the ability to bypass the proxy server via directly connecting to the Galaxy application's web port(s) would still be able to call this method. This is possible for anyone with direct login access to the server, or even remotely if the Galaxy application binds to all addresses (instead of just localhost) unless restricted by other means (e.g. a firewall). For Apache: <Location ~ "/history/switch_to_history.*"> Deny from all </Location> For nginx: location ~ /history/switch_to_history.* { deny all; } If using a proxy prefix (e.g. "/galaxy"), that prefix should be prepended to "/history". --nate Galaxy Team

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Call for papers for a special GCC2013 and Galaxy series in GigaScience
by Dave Clements 05 Apr '13

05 Apr '13

Hello all, I am pleased to inform you that talks presented at the 2013 Galaxy Community conference will be eligible for consideration to be published in the journal *GigaScience* and that BGI will generously cover the article processing fees for these articles. See the announcement below for details. thanks, Dave C -------------------------------- The 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> and BioMed Central <http://www.biomedcentral.com/> are announcing a special thematic series in *GigaScience <http://www.gigasciencejournal.com/> *, a new journal co-published in collaboration between BGI Shenzhen<http://www.genomics.cn/en/index> and BioMed Central <http://www.biomedcentral.com/> focused on studies utilizing large-scale datasets and workflows. Galaxy<http://galaxyproject.org/> is an open, web-based platform for data intensive biomedical research allowing their growing community of users to reproduce and share analyses. All accepted oral presentations from the meeting will be eligible for consideration in the series, and working with the scientific committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers#Scientific_Committee>, peer review will be coordinated, thorough and timely. BGI has been generously covering the open-access article-processing charges<http://www.gigasciencejournal.com/about/apcfaq> for the journal’s launch, and this offer will be extended to all submissions from the 2013 conference. Covering the themes of the conference, discussion and research is considered highlighting best practice for local Galaxy installation, management and use, as well as interesting tools, data sources, or novel uses of Galaxy. Addressing many of the goals of Galaxy to enable more accessible, reproducible, and transparent genomic science, submissions can utilize a novel format, where all of the workflows, tools and supporting data can be hosted and integrated into accepted papers using independently citable digital object identifiers<http://en.wikipedia.org/wiki/Digital_object_identifier> from the journal's Giga-Galaxy server <http://galaxy.cbiit.cuhk.edu.hk/> and GigaDB database <http://gigadb.org/>. Please contact the conference organizers <gcc2013-sci(a)galaxyproject.org> or GigaScience editors <editorial(a)gigasciencejournal.com> for further information, or submit a manuscript<http://www.gigasciencejournal.com/authors/instructions/research> or conference abstract<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts>, mentioning you would like to be considered in the series. The deadline for consideration for oral presentations to the meeting is 12th April, but later submissions for exceptional poster presentations (deadline 3rd May) and related work utilizing Galaxy may also be considered for the open series<http://www.gigasciencejournal.com/series> . Scott Edmunds Executive Editor *GigaScience <http://www.gigasciencejournal.com/>* -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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