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September 2014 Galaxy News
by Dave Clements 29 Aug '14

29 Aug '14

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Galaxy Events in Europe This Fall - Lots of them.
by Dave Clements 26 Aug '14

26 Aug '14

Hello all, There are several Galaxy related events in Europe this fall. These events are a great way to meet other Galaxy users and developers and learn and share best practices. Events start with ECCB and then wander the continent ending in Italy in November. If you are interested in learning more about Galaxy and/or the community, then please give these a look. Date Topic/Event Venue/Location Contact September 6-10 At least one tutorial, a panel of European Public Galaxy Instances, and 5 posters <https://wiki.galaxyproject.org/Events/ECCB2014> *European Conference on Computational Biology (ECCB'14) <https://wiki.galaxyproject.org/Events/ECCB2014>*, Strasbourg, France Presenters <https://wiki.galaxyproject.org/Events/ECCB2014> September 11 *Tools integration on Galaxy <http://go4bioinformatics.genouest.org/integration-doutils-dans-la-plateform…>* This event is now full. Galaxy User Group Grand Ouest <https://www.e-biogenouest.org/groups/guggo>, Rennes, France Cyril Monjeaud <https://www.e-biogenouest.org/members/1005>, Yvan Le Bras <https://www.e-biogenouest.org/members/1003> September 15 *Fourth GUGGO meeting <http://www.biogenouest.org/agenda/evenement/groupe-de-travail-des-utilisate…>* Galaxy User Group Grand Ouest <https://www.e-biogenouest.org/groups/guggo>, Rennes, France Cyril Monjeaud <https://www.e-biogenouest.org/members/1005>, Yvan Le Bras <https://www.e-biogenouest.org/members/1003> September 23-25 *Analisi dati Next Generation Sequencing con Galaxy <http://www.bioinformatica.crs4.it/next_generation_sequencing_course_with_ga…>* Cagliari, Italy CRS4 <ngs-courses(a)crs4.it> September 24 *Introduction to Galaxy - Data Manipulation and Visualisation <http://training.csx.cam.ac.uk/event/1222231>* University of Cambridge, United Kingdom Anne Pajon, Jing Su September 25 *RADseq analysis using STACKS on Galaxy <http://go4bioinformatics.genouest.org/analyse-de-donnees-de-type-rad-par-le…>* Galaxy User Group Grand Ouest <https://www.e-biogenouest.org/groups/guggo>, Rennes, France Yvan Le Bras <https://www.e-biogenouest.org/members/1003>, Cyril Monjeaud <https://www.e-biogenouest.org/members/1005> September 30 - October 2 *RNA-Seq & ChIP-Seq analysis course using Galaxy <http://www.fc3bio.fr/Analyse-des-donnees-RNA-seq-et-ChIP-seq-sequencage-hau…>* PRABI <http://www.prabi.fr/>, Lyon, France Navratil V <navratil(a)prabi.fr>., Oger C. <oger(a)prabi.fr>, Veber P. <veber(a)prabi.fr>, Deschamps C. <deschamps(a)prabi.fr>, Perriere G. <perriere(a)prabi.fr> September 30 - October 2 Galaxy Training and Demo Day <https://wiki.galaxyproject.org/Events/Switzerland2014/trainingday> Bern (Switzerland) Hans-Rudolf Hotz <https://wiki.galaxyproject.org/HansrudolfHotz> and Bjoern Gruening <https://wiki.galaxyproject.org/BjoernGruening> *(second Swiss) Galaxy Workshop <https://wiki.galaxyproject.org/Events/Switzerland2014>* SyBIT Tech Day, Bern (Switzerland) *German Galaxy Developers Day <https://wiki.galaxyproject.org/Events/Germany2014>* Freiburg (Germany) November 18-20 *Analisi dati Next Generation Sequencing con Galaxy <http://www.bioinformatica.crs4.it/training>* Cagliari, Italy CRS4 <ngs-courses(a)crs4.it> Europe does not have a monopoly on events in the coming months. There are also events in Australia and North America, See the Galaxy Events Page <https://wiki.galaxyproject.org/Events> for a complete list. Cheers / Au revoir / Ciao / Auf Wiedersehen, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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August 11, 2014 Galaxy Distribution
by Jennifer Jackson 15 Aug '14

15 Aug '14

August 11, 2014 Galaxy Distribution <http://wiki.galaxyproject.org/News/2014_08_11_Galaxy_Distribution> / <https://www.docker.com/>/ _Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2014_08_11>___ /Highlights:/// .Security alert <http://tinyurl.com/nhgmbc5>from July 31st, upgrade now .Citations <http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E…>: DOIs, bibtex, and much much more . Docker, docker,DOCKER <http://wiki.galaxyproject.org/Admin/Tools/Docker>. You voted, we've/got it/, with a little help from our friends (you!) . Significant Workflow, API, Job, Tool Shed, and Dataset management updates . Fixes, tunings, plus just a drop of ? Gossip *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_2014.06.02 /Thanks for using Galaxy!/ The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam>

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Announcing the UK Galaxy Community
by Dave Clements 14 Aug '14

14 Aug '14

Dear UK Galaxy-devs, We're delighted to announce the launch of the UK Galaxy Community. Please visit the site and have a look around: http://galaxy-community.org.uk/ The aims of Galaxy-UK are: - To bring the Galaxy community in the United Kingdom closer together - Identify and address the needs of the community - Encourage interaction and collaboration. Galaxy-UK is also an information hub for events such as: - UK based Galaxy training courses - UK based talks involving Galaxy - Information on the location of UK Galaxy servers - Anything else that might be pertinent to bring the UK Galaxy users/admins together as a community We will be organising both online meetings and physical meetings, so keep an eye on the site for these events. Best wishes, The Galaxy-UK Team. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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August 2014 Galaxy Newsletter
by Dave Clements 02 Aug '14

02 Aug '14

Hello all, The August 2014 Galaxy Update Newsletter <https://wiki.galaxyproject.org/GalaxyUpdates/2014_08> is out. Here's a preview of what's inside: - GCC2015 will be held in Norwich, United Kingdom, 6-8 July 2015 <https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#GCC2015:_Norwich.2C_Un…> - GCC2014 was a tremendous success <https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#GCC2014_Report>. Watch the talks, review the slides, posters, and BoF writeups. - ISMB and BOSC 2014 slides, posters and videos <https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#Galaxy_.40_ISMB_and_BO…> too. - 53 new papers <https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#New_Papers> - One new public server (IM-PET) <https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#New_Public_Servers> - Who's hiring? <https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#Who.27s_Hiring> It turns out that lots of places are. Happy August, 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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Galaxy Security Vulnerability
by Nate Coraor 31 Jul '14

31 Jul '14

A security vulnerability was recently discovered by Inge Alexander Raknes that would allow a malicious person to execute arbitrary code on a Galaxy server. The vulnerability was in a method that uses Python "pickle" functionality to decode state information from tool forms. Because pickles can be used to instantiate arbitrary Python objects, tool states could be constructed to exploit this vulnerability. Because this vulnerability allows for arbitrary code execution, administrators are strongly encouraged to apply this fix IMMEDIATELY. We have tried to make it as easy and quick as possible for server administrators to update their Galaxy instances. The fix has been applied to every stable release from 2013.01.13 until the tip, so it is possible to get this fix on older releases without updating to a newer feature release. You can do this by identifying your current release and updating to the `latest_<release_date>` tag corresponding to your release. For example, if you are running release_2013.11.04 (or a subsequent commit to the stable branch of Galaxy between release_2013.11.04 and release_2014.02.10), you can update with: % hg pull % hg update latest_2013.11.04 For the changes to take effect, YOU MUST RESTART ALL GALAXY SERVER PROCESSES. If you do not want to pull any upstream changes, we have also created a standalone patch that fixes this problem, with multiple versions depending on your current Galaxy release: - pickle-2013.11.04.patch - This patch should apply cleanly (with offset/fuzz) to releases from 2013.11.04 up to the current stable tip. Available at: https://depot.galaxyproject.org/patch/pickle-2013.11.04.patch - pickle-2013.01.13.patch - This patch should apply cleanly (with offset/fuzz) to releases from 2013.01.13 up to 2013.08.12, and possibly older versions of Galaxy as well. Available at: https://depot.galaxyproject.org/patch/pickle-2013.01.13.patch If you happen to be running a very recent revision on the default branch or the newly created next-stable branch, a pickle-default.patch file exists at the same place. For older releases or instances with conflicting local modifications, manual application of the patch should not be difficult as it only includes a few small changes. To apply the patch, navigate to the root of your Galaxy directory, then run (replacing <url_to_patch> with the URL above that is correct for your release): % wget -O pickle.patch <url_to_patch> or: % curl -o pickle.patch <url_to_patch> and then: % patch -p1 < pickle.patch patching file lib/galaxy/util/__init__.py Hunk #1 succeeded at 575 with fuzz 2 (offset -113 lines). patching file lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py Again, for the changes to take effect, YOU MUST RESTART ALL GALAXY SERVER PROCESSES. The Galaxy Team would like to extend special thanks to Inge Alexander Raknes and colleagues, who privately disclosed the vulnerability, with a full analysis and proof of concept. Credit for the fix and subsequent testing goes to my fellow Galaxy Team members John Chilton and Dannon Baker. On behalf of the Galaxy Team, --nate

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2014 Galaxy Community Conference June 6 Registration Deadline (this Friday)
by Dave Clements 04 Jun '14

04 Jun '14

Hello all, Regular registration for the 2014 Galaxy Community Conference (GCC2014, https://wiki.galaxyproject.org/Events/GCC2014) closes this Friday, June 6. After that late registration is still open, but registration rates *go up 100%.* GCC2014 is all about high-throughput biology. It's in Baltimore, from June 30 through July 2. The full program is posted, and includes - Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> - 15 sessions on 12 topics in 5 parallel tracks with topics ranging from *Visualizing NGS data *to* Galaxy installation and administration* - 26 talks <https://wiki.galaxyproject.org/Events/GCC2014/Program#Day_1:_Main_Meeting.2…> including a keynote by Steven Salzberg, and 25 other talks by researchers and industry leaders - 25 Posters <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts#Poster_Abstracts> - and counting - we still have space for a few more <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts#Abstract_Submission> - Lightning Talks - Present your rsesarch in two fast paced sessions. - Birds-of-a-Feather <https://wiki.galaxyproject.org/Events/GCC2014/BoFs> - Gather with other researchers with common interests and challenges (and propose one <https://wiki.galaxyproject.org/Events/GCC2014/BoFs#Want_to_plan_a_BoF.3F> for your own area of interest) - The first ever GCC Hackathon <https://wiki.galaxyproject.org/Events/GCC2014/Hackathon> (only 8 spaces left) Please do let us know if you have any questions. We would love to see you in Baltimore. Thanks, Dave Clements > *2014 Galaxy Community Conference (GCC2014) > <http://galaxyproject.org/GCC2014>* http://galaxyproject.org/GCC2014 > June 30 - July 2, 2014 > Homewood Campus > <http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…> > > Johns Hopkins University > <http://jhu.edu/> Baltimore, Maryland > <http://visitors.baltimorecity.gov/>, United States -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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June 2, 2014 Galaxy Distribution
by Jennifer Jackson 02 Jun '14

02 Jun '14

June 2, 2014 Galaxy Distribution <http://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution> *News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2014_06_02>**Highlights:* * Dataset Collections introduced * Changes to database build (dbkey) organization * Enhancements to Tool configuration and Workflow options * Trackster, User Interface, and Admin panel upgrades * Significant updates to Admin and Job functionality * Tool Shed repository and API additions * Data updates plus new Security features and Bug fixes * new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update latest_2014.06.02 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>* * /Thanks for using Galaxy!/ The Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam>

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June 2014 Galaxy Update Newsletter: GCC2014 registration closes in 1 week!
by Dave Clements 30 May '14

30 May '14

Hello all, The June 2014 Galaxy Update Newsletter <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06> is out! There's a lot going on in the project and the community right now. The big news for the coming month is - *GCC2014 registration closes June 6! <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#GCC2014:_June_30_-_Jul…>* - (OK, that's a lie, but after June 6, late registration rates kick in, and you really don't want to pay those.) - *GCC2014 starts June 30 <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#GCC2014:_June_30_-_Jul…>!* - *The first ever GCC Hackathon starts June 28 <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy_Hackathon_at_GC…>!* - After a very long and productive life, the *Galaxy-User mailing list is retiring on June 6* <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy-User_Being_Reti…>. (Don't worry. It's been replaced by Galaxy Biostar <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy-User_Being_Reti…> .) There are also at least 14 other Galaxy related events <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Other_Events> in the next two months in Thailand, Canada, France, the United States, Italy, the Netherlands, Australia, and Brazil. And, in the past month there were: - 49 new papers <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#New_Papers> - One new public server (deepTools) <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#New_Public_Servers> - One new Galaxy deployment description (deepTools) <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy_Community_Hubs> - and a stunning number of ToolShed contributions <https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#ToolShed_Contributions> Please let us know if you have anything to include in the July newsletter, and we will see you in Baltimore! Dave Clements and the Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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GCC2014 Early Registration closes this Friday, May 23
by Dave Clements 20 May '14

20 May '14

Hello all, This just a reminder that early registration<https://wiki.galaxyproject.org/Events/GCC2014/Register> for the 2014 Galaxy Community Conference (GCC2014)<https://wiki.galaxyproject.org/Events/GCC2014> *closes this Friday, May 23* Register early and *avoid paying 70% more for regular registration costs.* Early registration is downright affordable, with combined registration (Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main meeting) starting at $140 for post-docs and students. Registering early assures you a place at the conference and also a spot in the Training Day workshops<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay>you want to attend. And ... - The program <https://wiki.galaxyproject.org/Events/GCC2014/Program> , and abstracts <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> for all accepted talks are now available. - Registration for the GCC2014 hackathon<https://wiki.galaxyproject.org/Events/GCC2014/Hackathon> is also open (and also has limited capacity - register for that now too<https://wiki.galaxyproject.org/Events/GCC2014/Hackathon> ) - We are pleased to have Penguin Computing<http://www.penguincomputing.com/>as a Silver Sponsor for GCC2014 You are strongly encouraged to register this week. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Thanks a bunch, and hope to see you in Baltimore! Dave C -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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