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March 2015 Galaxy Release (v 15.03)
by Jennifer Hillman-Jackson 17 Mar '15

17 Mar '15

*March 2015 Galaxy Release (v 15.03)* <https://wiki.galaxyproject.org/News/2015_03_GalaxyRelease> [image: width=175] <http://getgalaxy.org/> Complete Release Notes <http://wiki.galaxyproject.org/DevNewsBriefs/2015_03> Highlights - *Release Versioning <https://wiki.galaxyproject.org/DevNewsBriefs/2015_03#Release_Versioning>* - Starting with this distribution, an updated Galaxy release versioning system has been implemented. The versioning scheme is Ubuntu-style <https://wiki.ubuntu.com/Releases>. *Github <https://wiki.galaxyproject.org/DevNewsBriefs/2015_03#Github>* - Galaxy development has moved to Github, but stable/release changes are mirrored to Bitbucket. Deployers can continue to use Bitbucket as they have done in the past. Release branches discussed in the full release notes. *Tool Redesign <https://wiki.galaxyproject.org/DevNewsBriefs/2015_03#Tool_Redesign>* - Much of Galaxy’s core tool set has been redesigned. Several contain new functionality. These tools are included in the Tool Shed <http://usegalaxy.org/toolsehd> and many are ready for use on Galaxy Main <https://wiki.galaxyproject.org/Main>. Get the Galaxy Release [image: getgalaxy] <http://getgalaxy.org/> *getgalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy>* *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_15.03 *Thanks for using Galaxy!* The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- Jennifer Hillman-Jackson http://galaxyproject.org

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The March 2015 Galaxy News
by Dave Clements 02 Mar '15

02 Mar '15

Hello all, As always, it's a busy time in the Galaxy <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03>. The March 2015 Galaxy News <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03> is out, and it's chock full of information. Here are some of the highlights. *UseGalaxy.org Update <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#UseGalaxy.org_Update>:* A refresh of UseGalaxy.org <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#UseGalaxy.org_Update> is underway. Find out what's changing in a new screencast. *2015 Galaxy Community Conference (GCC2015) <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#GCC2015:_6-8_July.2C_N…>* [image: Sponsor GCC2015] <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#GCC2015:_6-8_July.2C_N…> The event schedule for GCC2015 has been released, and it features a few new events as well as all of the familiar ones: - Code Hackathon <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Code_Hackathon>, 4-5 July - Data Wrangling Hackathon <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Data_Wrangling_Hackath…>, 4-5 July (*new*) - Training SunDay <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Training_SunDay>, 5 July (*new*) - Training Day <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Training_.28Mon.29Day>, 6 July - GCC Meeting <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Abstract_Submission_is…>, 7-8 July In addition, the workshop schedules for the *new* Training SunDay <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Training_SunDay>, and the returning Training Day <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Training_.28Mon.29Day> have been finalised. A record 15 topics will be covered in 18 sessions over two days of training. There are topics on using Galaxy, interacting with it programmatically, and deploying, administering, and extending Galaxy. No matter what you do with Galaxy, there are workshops for you. Abstract submission for oral and poster presentations is now open <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Abstract_Submission_is…>. We again have an arrangement with GigaScience that any oral or poster presentation will also be eligible for consideration for publication in the GigaScience "Galaxy: Data Intensive and Reproducible Research" series (first announced for GCC2013). Finally, registration is *not* open yet, but the list of registration packages and their costs <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Early_Registration_ope…> have been. Early registration is very affordable and starts at less than £40 per day for students and postdocs. *Other Events <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Other_Events>* And there is no shortage of other upcoming events either, including RNA-Seq and ChIP-Seq Analysis with Galaxy, UC Davis, March 23-26 <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#RNA-Seq_and_ChIP-Seq_A…>, and at least 12 other events in the next 2 months <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Other_Events>. *Lots of other news <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03>* In addition, there is news on: - 82 new publications <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#New_Papers>, including 7 highlighted ones - Summary of the Fall 2014 Galaxy Community Questionnaires <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Fall_2014_Questionnair…> - An introduction to Gravity <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Gravity>, a process manager (supervisor) for Galaxy servers. - Who's Hiring <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Who.27s_Hiring> - Whale Shark! <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Whale_Shark> - Planemo 0.5.0 released <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Planemo_0.5.0> - Two new Community Log Board entries <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Galaxy_Community_Hubs> - *Galaxy on GitHub! <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Galaxy_GitHub>* Come and join us in developing Galaxy! - And, other news <https://wiki.galaxyproject.org/GalaxyUpdates/2015_03#Other_News> as well. 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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GCC2015 Abstract Submission is Open
by Dave Clements 25 Feb '15

25 Feb '15

Hello all, *We are pleased to announce that abstract submission for Oral and Poster Presentations <http://gcc2015.tsl.ac.uk/Abstracts> at the 2015 Galaxy Community Conference (GCC2015) <http://gcc2015.tsl.ac.uk/> is now open.* Abstract submission <http://gcc2015.tsl.ac.uk/Abstracts> for oral presentations closes 10 April, and poster submission closes 1 May. Poster authors will be notified of acceptance status within two weeks of submission, while oral presentation authors will be notified no later than 24 April. *Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about it.* *About GCC2015* GCC2015 <http://gcc2015.tsl.ac.uk/> is hosted by The Sainsbury Lab <http://www.tsl.ac.uk/>, in Norwich, United Kingdom <http://www.visitnorwich.co.uk/>, in July 2015. GCC has been expanded this year and will now offer two hackathons, two Training Days, and a two day conference <http://gcc2015.tsl.ac.uk/programme/>. The Training Days <http://gcc2015.tsl.ac.uk/training-day/> cover 15 different topics spanning the full Galactic spectrum of topics. *Take a look <http://gcc2015.tsl.ac.uk/programme/>.* Thanks, 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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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 14 Jan '15

14 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 14 Jan '15

14 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 06 Jan '15

06 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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