- galaxy-announce - lists.galaxyproject.org

GCC2014 Training Day Topic Voting open January 6-17
by Dave Clements 06 Jan '14

06 Jan '14

Hello all, What topics should be offered at the GCC2014 Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> ? Topics <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> for the GCC2014 Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> are selected by you, the Galaxy Community. For GCC2014 there are 19 nominated topics<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay#Nominated_Topics> to pick from. Your votes 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 January 17.* The Training Day schedule, including instructors, will be published before early registration opens on February 10. Vote now! <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> *About the GCC2014 Training Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay>:* The 2014 Galaxy Community Conference (GCC2014)<https://wiki.galaxyproject.org/Events/GCC2014> will start on June 30 with a Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> featuring 4 parallel tracks, each with three workshops, each of which are two and a half hours long, for a total of twelve sessions. There will be at least one complete track (3 consecutive workshops) 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 GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0

January 2014 Galaxy Update Newsletter
by Dave Clements 31 Dec '13

31 Dec '13

1 0

GCC2014 Training Day: Topic Nomination is now open
by Dave Clements 18 Dec '13

18 Dec '13

Hello all, Training Day topics are nominated by you <http://bit.ly/gcc2014tdnom>, the Galaxy Community. Please take a minute to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see - what was offered at GCC2013<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> , - what topics were nominated in 2013 <http://bit.ly/1i2j1gN>, and - the Events <http://wiki.galaxyproject.org/Events> and the Events Archive<http://wiki.galaxyproject.org/Events/Archive> pages. Nominated topics will be published on the Training Day<http://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> page as they come in. *Nominations close December 20*. Topics will be compiled into a uniform list by the GCC2014 Organizing Committee, and topics will be posted and voted on by the Galaxy Community, January 6-17. Nominate a topic now! <http://bit.ly/gcc2014tdnom> Topics will then be selected and scheduled based on topic interest, and the organizers' 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. See you in Baltimore! GCC2014 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2014/Organizers> --- *About GCC2014:* The 2014 Galaxy Community Conference (GCC2014)<http://galaxyproject.org/gcc2014>will be held at the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…> of Johns Hopkins University <http://jhu.edu/>, inBaltimore, Maryland<http://visitors.baltimorecity.gov/>, United States, from June 30 through July 2, 2014. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, keynotes, lightning talks and bird-of-a-feather gatherings, all about high-throughput biology and the tools that support it. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 1

December 2013 Galaxy Update
by Dave Clements 02 Dec '13

02 Dec '13

1 0

Next GalaxyAdmins Meetup: November 20
by Dave Clements 14 Nov '13

14 Nov '13

Hello all, The next GalaxyAdmins meetup will be Wednesday, November 20, at 10am US Central time. See the meetup page<http://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_11_20> for a link and directions for connecting to the meetup. *GCC2013 GalaxyAdmins BoF Followup* This is our first meetup since the GCC2013 GalaxyAdmins BoF<http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins> where we discussed what the group should focus on going forward, and what the Galaxy Project can do to support the group. As suggested at GCC2013, followup to that discussion will be the main topic for this meetup. We came out with several action items and one piece of unfinished business (leadership). Also, as suggested at the GCC2013 BoF, we would like to encourage discussion in the week before the meetup. Therefore, 1. Please review the notes from the GCC2013 GalaxyAdmins BoF<http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins> 2. Take a look at these two draft implementations of action items from that discussion: 1. Galaxy Deployment Pages<http://wiki.galaxyproject.org/Community/Deployments> 2. Galaxy Log Pages <http://wiki.galaxyproject.org/Community/Logs> And, if you see anything that you want to comment on please reply to this thread on the Galaxy-Dev list. I'll update other actions as the call gets closer. *Galaxy Project Update: Main moves to TACC* Nate Coraor will give the project update, focusing on the recent move of UseGalaxy.org to TACC. We hope to see (well, hear) you there, and please don't hesitate to ask if you have any questions. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0

Nov 04, 2013 Galaxy Distribution
by Jennifer Jackson 04 Nov '13

04 Nov '13

1 0

Security vulnerability in Galaxy filtering tools
by Nate Coraor 04 Nov '13

04 Nov '13

A security vulnerability was recently discovered by John Chilton with Galaxy's "Filter data on any column using simple expressions" and "Filter on ambiguities in polymorphism datasets" tools that can allow for arbitrary execution of code on the command line. The fix for these tools has been committed to the Galaxy source. The timing of this commit coincides with the next Galaxy stable release (which has also been pushed out today). To apply the fix and simultaneously update to the new Galaxy stable release, ensure you are on the stable branch and upgrade to the latest changeset: % hg branch stable % hg pull -u For Galaxy installations that administrators are not yet ready to upgrade to the latest release, there are three workarounds. First, for Galaxy installations running on a relatively new version of the stable release (e.g. release_2013.08.12), Galaxy can be updated to the specific changeset that that contains the fix. This will include all of the stable (non-feature) commits that have been accumulated since the 8/12 release plus any new features included with (and prior to) the 8/12 release, but without all of the new features included in the 11/4 release. Ensure you are on the stable branch and then upgrade to the specific changeset: % hg pull -u -r e094c73fed4d Second, the patch can be downloaded and applied manually: % wget -o security.patch https://bitbucket.org/galaxy/galaxy-central/commits/e094c73fed4dc66b589932e… and then: % hg patch security.patch or: % patch -p1 < security.patch Third, the tools can be completely disabled by removing them from the tool configuration file (by default, tool_conf.xml) and restarting all Galaxy server processes. The relevant lines in tool_conf.xml are: <tool file="stats/dna_filtering.xml" /> <tool file="stats/filtering.xml" /> The full 11/4 Galaxy Distribution News Brief will be available later today and will contain details of changes since the last release. --nate Galaxy Team

1 0

November 2013 Galaxy Update Newsletter
by Dave Clements 31 Oct '13

31 Oct '13

Hello all, The November 2013 Galaxy Update is out<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11> : *Highlights:* - Two new public Galaxy servers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#New_Public_Servers> : CoSSci: Complex Social Science Gateway<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#CoSSci:_Complex_Social_…> (which has *nothing* to do with biology), and BioCiphers Lab Galaxy<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#BioCiphers_Lab_Galaxy> . - 53 new papers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#New_Papers>, including "Expanding roles in a library-based bioinformatics service program: a case study," "DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data," and "Ten Simple Rules for Reproducible Computational Research" - Who's hiring<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Who.27s_Hiring> - Upcoming Events<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Other_Events>, including - Save these dates! GCC2014: June 30 - July 2, Baltimore<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#GCC2014:_June_30_-_July…> - Galaxy Day, December 4, Paris<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Galaxy_Day.2C_December_…> - UC Davis Bioinformatics Boot Camps<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#UC_Davis_Bioinformatics…> - Lifeportal launched at the University of Oslo<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Lifeportal_at_the_Unive…> - Tool Shed contributions<http://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Tool_Shed_Contributions> If you have anything you would like to see in the next *Galaxy Update<http://wiki.galaxyproject.org/GalaxyUpdates> *, please let us know. Dave Clements and the Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0

Please save these dates! GCC2014: June 30 - July 2
by Dave Clements 02 Oct '13

02 Oct '13

Hello all, The 2014 Galaxy Community Conference (GCC2014)<http://wiki.galaxyproject.org/Events/GCC2014> has been scheduled for June 30 through July 2, at the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…> of Johns Hopkins University <http://jhu.edu/>, in Baltimore, Maryland<http://visitors.baltimorecity.gov/>, United States. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference will also includes a*Training Day* offering in-depth topic coverage, across several concurrent sessions. See the GCC2013 web site<http://wiki.galaxyproject.org/Events/GCC2013> for an idea of what happens at a Galaxy Community Conference. See you next summer, GCC2014 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2014/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0

October Galaxy Update Newsletter is out
by Dave Clements 30 Sep '13

30 Sep '13

Hello all, The October 2013 Galaxy Update is out<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10> : *Highlights:* - A record *six new public servers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#New_Public_Servers> * - 44 new papers<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#New_Papers> - Open Positions<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Who.27s_Hiring> at nine different organizations - Upcoming Events<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Events>, lots of them in Australia<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Australia.21> plus 3 other continents<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#All_Those_Other_Contine…>. - Online materials from past events<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Online_Materials_from_P…>, including all GCC2013 videos on Vimeo <http://bit.ly/gcc2013vimeo> and course materials for the 2013 UC Davis Bioinformatics Short Course<http://bit.ly/16rAUkf>. The UC Davis course featured 5 great days of lecture and hands-on exercises. - More Tool Shed contributions<http://wiki.galaxyproject.org/GalaxyUpdates/2013_10#Tool_Shed_Contributions> than you can shake a stick at. If you have anything you would like to see in the next *Galaxy Update<http://wiki.galaxyproject.org/GalaxyUpdates> *, please let us know. Dave Clements and the Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0