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October 2014 Galaxy Newsletter
by Dave Clements 01 Oct '14

01 Oct '14

Hello all, A lot is happening in in the Galaxy in October, and a lot of good stuff happened in September too. Take a look at the October 2014 Galaxy Newsletter <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10> for the complete story, but here are some highlights: - *Galaxy needs your input! <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Galaxy_Needs_Your_Inpu…>* You may even get rewarded for your input ... - IRC channel to be logged <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#IRC_Channel_Policy_Cha…>, starting this month - Slides from ECCB'14 and upcoming events <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Events> - 71 new papers <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#New_Papers>, including 6 featured papers - Who's Hiring? <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Who.27s_Hiring> Lots of places, that's who - Two new public Galaxy Servers <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#New_Public_Servers> - New Deployment Catalog and Log Board entries <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Community_Galaxy_Hubs> - 36 new ToolShed repos <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contribution> - And a smattering of other news <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Other_News> too Happy October! 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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2014 Galaxy Questionnaire
by Dave Clements 30 Sep '14

30 Sep '14

Hello all, The Galaxy Project is preparing for our next grant cycle and we are seeking your feedback and comments on on all things Galaxy. We have created two questionnaires, each focused on a different way to interact with Galaxy: 1. *Galaxy User Questionnaire <https://docs.google.com/forms/d/1NT3ma2g7rR-mWA_vgOg2Ia_6VTFiZ86um2JhX2SecC…>* 2. *Galaxy Admin, Tool Developer, and Galaxy Developer Questionnaire <https://docs.google.com/forms/d/1lszXJ2lDJ2dYCWKXBk1qT1jO7XdDDfxXmGRCUMZFX2…>* Please take a few minutes and fill out the surveys that apply to you. The questionnaires are structured so you can skip topics (whole pages!) that don't apply to you, and every question is optional. *And, to thank you for your time and effort, the Galaxy Project will increase your storage quota on usegalaxy.org <https://usegalaxy.org/> by 50GB. *That's a 20% increase. Let your voice be heard (and, get some storage)! 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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Proposal: Create a public archive of the GalaxyProject IRC Channel
by Dave Clements 02 Sep '14

02 Sep '14

Hello all, We would like to change the logging policy for the #galaxyproject IRC channel <https://wiki.galaxyproject.org/GetInvolved#IRC_Channel>: - *Starting later this fall, the #galaxyproject IRC channel <https://wiki.galaxyproject.org/GetInvolved#IRC_Channel> will be logged online in a format that can be searched.* Currently, this channel is not logged anywhere. This change will only be made if the community agrees that a searchable online log would be an improvement. *If you have thoughts or comments on this proposal, then please post them to this Biostar thread <http://bit.ly/gxybs8804>*. In two weeks' time (around September 17, 2014), we'll summarize the discussion and publish a decision. *Proposal Details:* Starting sometime after community discussion ends (and assuming that discussion is favorable): 1. At least two weeks before the change: 1. Warnings will be added to the IRC channel information and on the wiki, that the log will be publicly archived as of the given start date. 2. The policy change will be announced on Galaxy Biostar <https://wiki.galaxyproject.org/Support/Biostar> and the Galaxy-Dev and Galaxy-Announce mailing lists <https://wiki.galaxyproject.org/MailingLists>. 2. On the launch date 1. The IRC channel (and the wiki) will be updated to clearly state that the IRC channel is publicly logged. 2. Announcements of the change will be posted to Biostar and the mailing lists. 3. IRC postings from the announcement onward will start showing up in the public log. 4. The IRC channel log will be included in the Galaxy search engines <http://galaxyproject.org/search/>. *Why now?* The project's IRC channel came up at the GalaxyAdmins BoF meetup <https://wiki.galaxyproject.org/Events/GCC2014/BoFs/GalaxyAdmins> at GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014>, where it was lauded as both a great resource, *and cursed because it is not archived anywhere.* An action item from that meetup is to propose this change. 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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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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