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Feb 10, 2014 Galaxy Distribution & News Brief
by Jennifer Jackson 11 Feb '14

11 Feb '14

Feb 10, 2014 Galaxy Distribution & News Brief <https://wiki.galaxyproject.org/News/2014_02_10_Galaxy_Distribution> // *CompleteNews Brief <https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10>* *Highlights:* * Visualization upgrades, including Trackster CSS styling * Multiple Tools migrated to the Tool Shed for a leaner distribution * Redesign of UI rendering: new icons, new font, history pane updates * API functionality upgrades featuring a new master admin API key and * Tool Shed updates a focus on repository metadata, displays, installs, and tests * Over 35 new community contributions added http://getgalaxy.org <http://getgalaxy.org/> http://bitbucket.org/galaxy/galaxy-dist http://galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/> new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable upgrade: $ hg pull $ hg update release_2014.02.10 /Thanks for using Galaxy!/ The Galaxy Team <https://wiki.galaxyproject.org/Galaxy%20Team>

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February 2014 Galaxy Update Newsletter
by Dave Clements 31 Jan '14

31 Jan '14

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Galaxy Australasia Workshop (GAW 2014), 24-25 March, Melbourne
by Dave Clements 17 Jan '14

17 Jan '14

Hello all, *We are pleased to announce the 1st Galaxy Australasia Workshop 2014 (GAW 2014) <https://wiki.galaxyproject.org/Events/GAW2014> will be held in Melbourne, Australia on 24 and 25th March 2014.* The Galaxy Australasia Workshop<https://wiki.galaxyproject.org/Events/GAW2014> is a great opportunity for you to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch <http://wp.csiro.au/css/> in Melbourne. GAW 2014 will also include poster session, keynote speakers. *You should attend to:* - Present your work! - Learn best practices for deploying Galaxy, defining and installing resources, and managing and moving large datasets. - Network with others in the Galaxy community who are facing similar challenges and using Galaxy and other tools to address them. - Learn what the Galaxy Project's plans are, and contribute to Galaxy's future direction. - Learn - how to visualize your data in Galaxy and use visualization to guide your analysis (visual analytics) - how to share, publish, and reuse your analyses with Galaxy - how to perform and enable your users to perform common, yet complex, analyses using Galaxy - when and how to use Galaxy on the Cloud *Topics will potentially include:* - Image analysis and processing using Galaxy. - RNAseq/ChIPseq/Variant Calling/RNA Quality Control. - Galaxy on the Research Cloud. - CSIRO galaxy service - partnership between science and IT. - Identifying proteins from mass spec data with Galaxy. *Call For Abstracts* Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should submit a brief one-page abstract and brief one-paragraph bio to the GAW2014 Organisers <gaw2014-org(a)groups.galaxyproject.org> *by February 15th, 2014.* Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance. Submissions should clearly state whether they are for: poster or oral presentation. Looking forward to seeing you all in Melbourne! GAW 2014 Organising Committee<https://wiki.galaxyproject.org/Events/GAW2014#Organising_Committee> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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GCC2014 Training Day Topic Voting open January 6-17
by Dave Clements 07 Jan '14

07 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/

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January 2014 Galaxy Update Newsletter
by Dave Clements 01 Jan '14

01 Jan '14

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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/

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December 2013 Galaxy Update
by Dave Clements 02 Dec '13

02 Dec '13

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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/

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Nov 04, 2013 Galaxy Distribution
by Jennifer Jackson 05 Nov '13

05 Nov '13

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Security vulnerability in Galaxy filtering tools
by Nate Coraor 05 Nov '13

05 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

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