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Galaxy Tool Shed security vulnerability
by Nate Coraor 23 Apr '15

23 Apr '15

*Please note: This notice affects Galaxy Tool Shed servers only. Galaxy servers are unaffected.* A security vulnerability was recently discovered by Daniel Blankenberg of the Galaxy Team that would allow a malicious person to execute arbitrary code on a Galaxy Tool Shed server. The vulnerability is due to reuse of tool loading code from Galaxy, which executes "code files" defined by Galaxy tool config files. Because the Tool Shed allows any user to create and "load" tools, any user could cause arbitrary code to be executed by the Tool Shed server. In Galaxy, administrators control which tools are loaded, which is why this vulnerability does not affect Galaxy itself. Although we recommend upgrading to the latest stable version (15.03.2), a fix for this issue has been committed to Galaxy versions from 14.08 and newer. If you are using Mercurial, you can update with (where YY.MM corresponds to the Galaxy release you are currently running): % hg pull % hg update release_YY.MM If you are using git, you can update with (assuming your remote upstream is set to https://github.com/galaxyproject/galaxy/) If you have not yet set up a remote tracking branch for the release you are using: % git fetch upstream % git checkout -b release_YY.MM upstream/release_YY.MM Otherwise: % git pull upstream release_YY.MM For the changes to take effect, *you must restart all Tool Shed server processes*. Credit for the arbitrary code execution fix also goes to my fellow Galaxy Team member Daniel Blankenberg. On behalf of the Galaxy Team, --nate

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GCC2015 Registration and Lodging Scholarship for US-Based Post-Docs and Students
by Dave Clements 21 Apr '15

21 Apr '15

Hello all, *We are pleased to offer registration <http://gcc2015.tsl.ac.uk/registration> and lodging <http://gcc2015.tsl.ac.uk/logistics/#Lodging> scholarships for GCC2015 for students and post-docs who are based in the United States, and who are members of historically underrepresented groups in life science research.* These scholarships cover registration costs <http://gcc2015.tsl.ac.uk/registration> for any GCC2015 events <http://gcc2015.tsl.ac.uk/proigramme> the recipients sign up for, and also covers lodging <http://gcc2015.tsl.ac.uk/logistics/#Lodging> during those events in the official conference lodging <http://gcc2015.tsl.ac.uk/logistics/#Lodging> on the nearby UEA campus. *The scholarships do not cover travel or other expenses.* To apply for a scholarship qualifying applicants need to 1. Submit a poster abstract <http://bit.ly/gcc2015sub>. *The deadline is May 1* 2. Have a faculty member / PI send a letter of recommendation to the Galaxy Community Fund Board <community-fund(a)lists.galaxyproject.org> no later than May 15. 3. Submit an application form <http://bit.ly/gcc2015scholarship>, no later than May 1. 4. Have sufficient funds to cover your travel and other expenses. Applicants will be notified of their scholarship status no later than May 19. Scholarships are funded by the *Galaxy Community Fund*. The Galaxy Community Fund was established with the surplus funds from GCC2014, and is currently administered by the GCC2014 organizers. Please do let us know if you have any questions, and we hope to see you at GCC2015 <http://gcc2015.tsl.ac.uk/>! Galaxy Community Fund Board <community-fund(a)lists.galaxyproject.org> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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GCC2015 Oral Presentation Abstract Submission closes 20 April
by Dave Clements 20 Apr '15

20 Apr '15

Hello all, Just a reminder that oral presentation abstract submission for GCC2015 closes on Monday, 20 April, 5 days from now. Poster submission closes 1 May. See http://gcc2015.tsl.ac.uk/Abstracts for more. The 2015 Galaxy Community Conference is an opportunity to share your work with 200+ other researchers working in data-intensive biology. GCC2015 features 2 days of (2 different) hackathons, 2 days of training, and 2 days of meeting, posters, presentations, birds of a feather, and networking. See http://gcc2015.tsl.ac.uk/ for more on GCC2015. Looking forward to seeing you in July in Norwich! Dave C. On Wed, Feb 25, 2015 at 12:04 AM, Dave Clements <clements(a)galaxyproject.org> wrote: > 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/ > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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April! Galactic News!
by Dave Clements 02 Apr '15

02 Apr '15

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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 29 Jan '15

29 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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