- galaxy-announce - lists.galaxyproject.org

Interested in hosting GCC2016?
by Dave Clements 03 Feb '15

03 Feb '15

Hello all, The Galaxy Community Conference has been held annually since 2010. This year's event (GCC2015) <http://gcc2015.tsl.ac.uk/> is being hosted by The Sainsbury Lab <http://tsl.ac.uk/> in Norwich, UK. *We are now seeking proposals from any organization interested in hosting GCC2016.* GCC draws 200+ participants from data-intensive life science research. Participants come from around the world, from all career stages, and do research spanning the tree of life. Universities, hospitals and medical schools, research organizations, and industry are all represented, including the largest and most influential organizations in the world. What do we need to host GCC, you ask? In approximately decreasing order of importance: - *Enthusiasm to plan and organize a 3+ day event for more than 200 people.* - Space for 4-6 parallel Training Day sessions, each able to accommodate from 25 to 75 participants. - Central meeting space with capacity for 250-300 people. - Affordability (or access to sponsorship funds; there's a reason we've always held GCC in academic settings) - Nearby space for breakouts, poster sessions and sponsors. - Nearby space for lunch, coffee breaks. - Good wifi for all events (that's 200+ people and their devices). - Space for a hackathon for 2 days before the event. - Easy to get to by air, from within the States, and from overseas - Nearby, affordable housing, or easy walking distance or easy public transport from lodging options to conference facilities - Close proximity to a pub and other social hubs. Hosts get copious (and enthusiastic) organizational support from Galaxy's Outreach Team (who have been helping to organize GCC since 2011), and even more copious gratitude (even *adulation!)* from the Galaxy Community. If you are interested in possibly hosting GCC2016 next summer then please contact Galaxy Outreach <outreach(a)galaxyproject.org>. Our goal is to announce the site at this year's conference in July. Hoping to work with you in 2016! 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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Galactic News!!! February 2015 Edition
by Dave Clements 30 Jan '15

30 Jan '15

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GCC2015 Training Day Topic Voting is open. Please vote!
by Dave Clements 19 Jan '15

19 Jan '15

Hello all,What topics should be offered at the GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/>? Topics <http://gcc2015.tsl.ac.uk/training-day/> for the GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/> are selected by you, the Galaxy Community. There are nominated topics <http://gcc2015.tsl.ac.uk/training-day/> spanning from basic usage to advanced deployment. No matter what you do with Galaxy, there are topics for you to choose from. Your vote will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. *Topic voting closes 30 January.* The Training Day schedule, including instructors, will be published before early registration opens in February. *Vote Now <http://gcc2015.tsl.ac.uk/training-day/>* ------------------------------ *About the GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/>:* The 2015 Galaxy Community Conference (GCC2015) <http://gcc2015.tsl.ac.uk/> will start on 6 July with a Training Day <http://gcc2015.tsl.ac.uk/training-day/> featuring parallel tracks, each with several multi-hour workshops. There will be at least one complete track about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances. As always, please let us know if you have any questions. Thanks, The GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers/> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Galaxy security vulnerabilities and 2015.01.13 Galaxy Stable Release
by Nate Coraor 13 Jan '15

13 Jan '15

A number of security vulnerabilities were recently discovered by Bartlomiej Balcerek and colleagues at the Wroclaw Centre for Networking and Supercomputing, which have been fixed in the current stable Galaxy release (2014.10.06). We have simultaneously created a new stable release (2015.01.13) today which includes these fixes as well as new features. Galaxy server administrators are STRONGLY encouraged to update their Galaxy servers to one of these releases immediately. The first vulnerability identified would allow a malicious person to execute arbitrary code on a Galaxy server. The vulnerability is due to gaps in Galaxy's command line template parameter sanitization. Although all form fields were sanitized for shell metacharacters, some other parameters that might be provided to tools on the command line (such as the input dataset name) were not. Because of this, dataset names and other fields could be constructed to exploit this vulnerability. Due to the severity of this specific vulnerability, the fix for it has been applied back to previous releases beginning with the January 13, 2013 release. The fix can be obtained by executing `hg pull && hg update latest_<YYYY>.<MM>.<DD>`, replacing the date with the date of the release currently in use. In addition to the code execution exploit, a number of cross-site scripting (XSS) vulnerabilities were identified by Bartlomiej which we have fixed in our new and previous stable releases. We only backport fixes for exploits that we believe allow an attacker to readily gain access to the Galaxy server to previous stable releases - nonetheless we consider these XSS vulnerabilities to be serious and would strongly recommend that public servers upgrade to at least the previous stable release, using the latest_2014.10.06 tag, to address them. The Galaxy Team also performed an audit to locate and fix any additional XSS vulnerabilities that might exist. Additional details on issues found and resolved can be found in the January 13, 2015 Galaxy Distribution News Brief at: https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13 To get the changes, for example, if you are running release_2014.10.06 (or a subsequent commit to the stable branch of Galaxy between release_2014.10.06 and release_2015.01.13), you can update with: % hg pull % hg update latest_2014.10.06 For the changes to take effect, YOU MUST RESTART ALL GALAXY SERVER PROCESSES. The Galaxy Team would like to extend special thanks to Bartlomiej Balcerek and colleagues, who privately disclosed the arbitrary code execution and XSS vulnerabilities, with a full report and proof of concepts. Credit for the arbitrary code execution fix goes to my fellow Galaxy Team member Daniel Blankenberg. The entire team worked to resolve the identified XSS issues and conduct the larger code audit. On behalf of the Galaxy Team, --nate

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January 13, 2015 Galaxy Distribution
by Jennifer Hillman-Jackson 13 Jan '15

13 Jan '15

*January 13, 2015 Galaxy Distribution* <https://wiki.galaxyproject.org/News/2014_01_13_Galaxy_Distribution> [image: width=175] <http://getgalaxy.org/> *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13>* Security Several *critical* security vulnerabilities were recently discovered by Bartlomiej Balcerek and colleagues at the Wroclaw Centre for Networking and Supercomputing. This stable Galaxy release contains fixes for those vulnerabilities <https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#Security>. *The Galaxy Team strongly encourages Galaxy server administrators to update their Galaxy servers immediately.* IPython Integration Thanks to the awesome work of community members Björn Grüning and Eric Rasche, Galaxy now features integration with the popular IPython project <https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#IPython_Integration>. The Galaxy-IPython <https://github.com/bgruening/galaxy-ipython> project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker. Tool Form Upgrade (for Beta Testing) In Galaxy's development branch, the basic tool from has been redesigned and modernized to address certain limitations in Galaxy's responsiveness when working with longer forms containing multiple parameter choices <https://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13#Tool_Form_Upgrade_.…>. This new tool form will become the default with the next release - but we are hoping tool author's and power users enable it and provide feedback during this release cycle in order to ensure it is working ideally when it becomes the default. Get The Distribution [image: getgalaxy] <http://getgalaxy.org/> *getgalaxy.org <http://wiki.galaxyproject.org/Admin/GetGalaxy>* *galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/>* *bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* *new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update latest_2015.01.13 *Thanks for using Galaxy!* The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- Jennifer Hillman-Jackson http://galaxyproject.org

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GCC2015 Training Day Topic Nominations are Open through January 6
by Dave Clements 05 Jan '15

05 Jan '15

Hello all, GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/> topics are nominated by you <http://bit.ly/gcc2015tdnom>, the Galaxy Community. Please take a few minutes to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one. If you are looking for ideas, see the topics nominated in 2013 <http://bit.ly/1i2j1gN> and 2014 <http://bit.ly/1s6NtMN>, and the Events <https://wiki.galaxyproject.org/Events> and the Events Archives <https://wiki.galaxyproject.org/Events/Archive> pages. Nominated topics will be published on the Training Day <http://gcc2015.tsl.ac.uk/training-day/> page as they come in. *Nominations close 6 January*. Topics will be compiled into a uniform list by the GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers>, and topics will be voted on by the Galaxy Community 12-23 January. Topics will then be selected and scheduled based on topic interest, and the organisers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. Cheers, GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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January 2015 Galaxy News!
by Dave Clements 05 Jan '15

05 Jan '15

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December 2014 Galaxy Newsletter
by Dave Clements 01 Dec '14

01 Dec '14

Hello all, As always there's a lot going on in the Galaxy this month. "Like what?" you say. Well, read the dang December Galaxy Newsletter <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12> we say! Highlights include: - Galaxy Day! In Paris! This Wednesday! <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Galaxy_Day:_3_December…> - Near Richmond, Virginia? There's a Galaxy Workshop at Virginia State U on December 12 <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Intro_to_Galaxy_Worksh…> . - GCC2015 needs sponsors <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#GCC2015:_6-8_July.2C_N…> ! - Other upcoming events <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Other_Events> on two continents - *96 new papers <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#New_Papers>*, including 6 highlighted papers, referencing, using, extending, and implementing Galaxy. - Job openings at 7+ organizations <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Who.27s_Hiring> - A new mailing list: Galaxy-Training <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#New_Galaxy-Training_Ma…> - 15 new ToolShed repositories from 10 contributors <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#ToolShed_Contributions> - And, 10 other juicy <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Other_News> (well maybe not *juicy*, but certainly not *crunchy*) bits of news <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Other_News> Happy December! Dave Clements and the *crisp* Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Galaxy Mailing Lists are moving
by Nate Coraor 11 Nov '14

11 Nov '14

Hello Galaxy Community, *Galaxy Mailing Lists are moving!* During the week of November 17-21, 2014, Galaxy mailing lists (including this one) will be migrated from lists.bx.psu.edu to lists.galaxyproject.org . This transition should be largely transparent to you, but there are a few things to be aware of: - List sender addresses and headers will change to reflect the updated domain: from bx.psu.edu to galaxyproject.org. Existing email filters you have set up may require adjustments. - Posts from lists.galaxyproject.org could be categorized as spam until you train your filtering method. - Mailing list archives and posting functionality will be briefly inaccessible during the migration. - The prior bx.psu.edu list posting email addresses will continue to accept email, which will be forwarded to the new list addresses. As always, you can manage your subscription for any Galaxy mailing list by following the link instructions at the bottom of this announcement. If you should notice any problems after the migration, please do not hesitate to let us know, via email to both "<list>-owner(a)lists.galaxyproject.org" (after the move) and to myself. Thanks, --nate, and the Galaxy Team

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(no subject)
by Dave Clements 03 Nov '14

03 Nov '14

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