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August 2013 Galaxy Update Newsletter is out
by Dave Clements 31 Jul '13

31 Jul '13

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(no subject)
by Dave Clements 30 Jun '13

30 Jun '13

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Galaxy Security Notification
by Nate Coraor 12 Jun '13

12 Jun '13

A security vulnerability was recently discovered by Björn Grüning with Galaxy's "user impersonation" feature that can expose an administrator's active history to users whom they impersonate. Only Galaxy instances with `allow_user_impersonation = True` set in their configurations are affected, and only if an administrator makes use of the impersonation feature. By default, user impersonation is disabled. A fix (id: 9d42f1e32efb) has been provided in the stable branch of Galaxy. To apply the fix, ensure you are on the stable branch and upgrade to the latest changeset: % hg branch stable % hg pull -u For Galaxy installations on relatively old versions that administrators are not yet ready to upgrade, there are three workarounds. First, the patch can be downloaded and applied manually: % wget -o security.patch https://bitbucket.org/galaxy/galaxy-central/commits/9d42f1e32efb654fda1e011… and then: % hg patch security.patch or: % patch -p1 < security.patch Second, the impersonation feature can be disabled by setting the following option in Galaxy's configuration file: allow_user_impersonation = False In all of the above cases, the Galaxy server process(es) must be restarted for the change to take effect. Third, the feature can be left enabled and unpatched, and the vulnerability can be worked around by educating administrators who use the feature. As long as a new history is created by the administrator prior to switching to the impersonated user, no data will be exposed to the impersonated user. --nate Galaxy Team

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GCC2013 Regular Registration closes June 14
by Dave Clements 04 Jun '13

04 Jun '13

Hello all, This is a reminder that registration<http://wiki.galaxyproject.org/Events/GCC2013/Register>for the 2013 Galaxy Community Conference (GCC2013<http://wiki.galaxyproject.org/Events/GCC2013>) closes June 14*, just ten days from today. *Registering now<http://wiki.galaxyproject.org/Events/GCC2013/Register>avoids the 100% late registration surcharges, and guarantees you a spot in the Training Day sessions<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay>you want to take. *Registration is still a bargain with the full 3-day registration starting at ~ €165 for post-docs and students (that is just €55 per day). The program <http://wiki.galaxyproject.org/Events/GCC2013/Program> features 15 Training Day sessions<http://wiki.galaxyproject.org/Events/GCC2013/Program#Day_0:_Training_Day.2C…> in 5 tracks on 12 different topics, 25 Talks<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Talk_Abstracts> on topics ranging from Reproducibility<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FA…> to Exploiting Galaxy<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FA…> , 23 Posters<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Poster_Abstracts> (and counting), 2 Lightning Talk sessions, and a end-of-conference event at an historic venue high above Oslo. GCC2013 is a great opportunity to share best practices from and network with other researchers also facing the challenges of data-intensive biology. Ser frem til å se deg i Oslo! GCC2013 Organizing Committee PS: and please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> . * Not June 7, as had been stated earlier in several places. -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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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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