- galaxy-announce - lists.galaxyproject.org

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 01 Aug '14

01 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 19 May '14

19 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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May 2014 Galaxy News Update
by Dave Clements 30 Apr '14

30 Apr '14

Hello all, The May 2014 Galaxy Update Newsletter<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05> is out! There's a lot going on in the project and the community right now. The big news in the past month is the move from the Galaxy-User mailing list to Galaxy Biostar<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Biostar> for user support. This has been running for a week now, and has been very well received. The other big news is upcoming events. *Early registration for GCC2013 closes May 23 <https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#GCC2014:_June_30_-_Jul…>* . Register now <https://wiki.galaxyproject.org/Events/GCC2014/Register> and save more than 70% on registration costs, and Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> registration is an additional 55% off if you register for both at the same time. We are also pleased to announce this year's keynote speaker<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Keynote_Speaker:_Steve…> and the first ever GCC Hackathon<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Hackathon_at_GC…> . There's also a Galaxy UK Tour<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#UK_May_2014_Galaxy_Tour> which is visiting Norwich and Edinburgh in May, and there are at least 17 other Galaxy related events<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Other_Events> in the next 70 days in Norway, France, *online*, Croatia, Thailand, Canada, the US, the Netherlands, and Australia As always, there are new papers<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Papers> (47 of them, including four we highlighted), new public Galaxy Servers<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Public_Servers> (Globus Genomics Proteomics<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Globus_Genomics_Proteo…> and SunLab Galaxy<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#SunLab> ), new jobs<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Who.27s_Hiring> (7 postings in 6 countries), new tools in the project ToolShed<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Project_ToolShe…> (um, *lots*), and a new public ToolShed<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Public_Tool_Sheds> (at the Dutch Techcentre for Life Sciences (DTL) <http://www.dtls.nl/dtl/>. 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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Announcing the Galaxy Biostar Forum
by Jennifer Jackson 23 Apr '14

23 Apr '14

Dear Galaxy Community, Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org! We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool help. Whether on usegalaxy.org, a Cloudman instance, or any other Galaxy, if you have something to say about Using Galaxy, this is the place to do it! Current integration with usegalaxy.org * We imported the whole history of galaxy-user(a)bx.psu.edu mailing list into Biostar * If you access Galaxy Biostar from usegalaxy.org (menu Help/Galaxy Biostar) you will be automatically logged in. * A Galaxy Biostar account will be created for you if it did not previously exist. To obtain this account’s password please use the password reset feature of Galaxy Biostar (https://biostar.usegalaxy.org/accounts/password/reset/) * When you have a question, search Biostar directly from any Galaxy tool page. Read more about how to get started at https://wiki.galaxyproject.org/Support/Biostar Roll-out phase * Galaxy Biostar is available at http://biostar.usegalaxy.org and will be our primary avenue for support * The galaxy-user(a)bx.psu.edu mailing list will continue to be supported during the transition but starting now please use the biostar.usegalaxy.org forum to ask all questions about using Galaxy. * Please do not double post to both Galaxy Biostar and galaxy-user(a)bx.psu.edu * Send us feedback through the forum's post "Welcome to Biostar" to tell us what you think. What’s next * Notice will be given when the galaxy-user(a)bx.psu.edu mailing list is retired. * Archives of galaxy-user(a)bx.psu.edu will remain accessible. We hope you will like the change and look forward to any feedback you may have. Thank you for using Galaxy! The Galaxy team

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Announcing the Galaxy Biostar Forum
by Jennifer Jackson 23 Apr '14

23 Apr '14

* Dear Galaxy Community, Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org <https://biostar.usegalaxy.org/>! We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool help. Whether on *usegalaxy.org <http://usegalaxy.org>*, a***<https://usegalaxy.org/cloud>**Cloudman <http://usegalaxy.org/cloud> *instance, or any other <https://wiki.galaxyproject.org/PublicGalaxyServers> *Galaxy <http://getgalaxy.org>*, if you have something to say about Using Galaxy, this is the place to do it! Current integration with usegalaxy.org * We imported the whole history of galaxy-user(a)bx.psu.edu mailing list into Biostar * If you access Galaxy Biostar from *usegalaxy.org* <http://usegalaxy.org> (Top*m*enu: "Help ->Galaxy Biostar")you will be automatically logged in. A Galaxy Biostar account will be created for you if it did not previously exist. To obtain this account's password please use the password reset feature of Galaxy Biostar (https://biostar.usegalaxy.org/accounts/password/reset/) * When you have a question, search Biostar directly from any Galaxy tool page. Read more about how to get startedat https://wiki.galaxyproject.org/Support/Biostar Roll-out phase * Galaxy Biostar is available at *http://biostar.usegalaxy.org*and will be our primary avenue for support * The galaxy-user(a)bx.psu.edu mailing list will continue to be supported during the transitionbut starting now please use the biostar.usegalaxy.org <http://biostar.usegalaxy.org>forumto ask all questions about using Galaxy. * Please do not double postto both Galaxy Biostar and galaxy-user(a)bx.psu.edu * Send us feedback through the forum's post *"Welcome to Biostar"* to tell us what you think. What's next * Notice will be given when the galaxy-user(a)bx.psu.edu mailing list is retired. * Archives of galaxy-user(a)bx.psu.edu will remain accessible. We hope you will like the change and look forward to any feedback you may have. Thank you for using Galaxy! *Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam>* *

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