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subscription
by Oya Uyguner 11 Feb '13

11 Feb '13

Dear Sir/Madam, I would like to subscribe Galaxy-User and Galaxy-Dev. I thank you very much for your consideration. Z. Oya Uyguner, PhD Istanbul Medical Faculty, Department of Medical Genetics Bu elektronik posta ve beraberinde iletilen bütün dosyalar sadece göndericisi tarafindan alinmasi amaçlanan yetkili gerçek ya da tüzel kisinin kullanimi içindir.Eger söz konusu yetkili alici degilseniz bu elektronik postanin içerigini açiklamaniz, kopyalamaniz, yönlendirmeniz ve kullanmaniz kesinlikle yasaktir ve bu elektronik postayi derhal silmeniz gerekmektedir. ISTANBUL ÜNIVERSITESI bu mesajin içerdigi bilgilerin dogrulugu veya eksiksiz oldugu konusunda herhangi bir garanti vermemektedir. Bu nedenle bu bilgilerin ne sekilde olursa olsun içeriginden, iletilmesinden, alinmasindan ve saklanmasindan sorumlu degildir. Bu mesajdaki görüsler yalnizca gönderen kisiye aittir ve ISTANBUL ÜNIVERSITESI'nin görüslerini yansitmayabilir. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------! ----------------------- This message and attachments are confidential and intended solely for the individual(s) stated in this message.This email is not intended to impose nor shall it be construed as imposing any legally binding obligation upon ISTANBUL UNIVERSITY and/or any of its subsidiaries or associated companies. Neither ISTANBUL UNIVERSITY nor any of its subsidiaries or associated companies gives any representation or warranty as to the accuracy or completeness of the contents of this email. ISTANBUL UNIVERSITY will not be held liable to any person resulting from the use of any information contained in this email and will not be liable to any person who acts or omits to do anything in reliance upon it.

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Galaxy February 8, 2013 Distribution & News Brief
by Jennifer Jackson 08 Feb '13

08 Feb '13

Galaxy Feb 8, 2013 Distribution & News Brief <http://wiki.galaxyproject.org/News/2013_02_08_GalaxyNewsBrief> *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08> * *Highlights:* * /Improvements/ to our release process <http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08#Improvements_to_Rele…>. *Release tag must be used in the hg update command to upgrade*. More at *usegalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy>*. * Tool Shed /Complex repository dependencies/ <http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_reposi…> are introduced, streamlining core dependency use across individual tools. * Also updated in the Tool Shed: multiple repository installation, dependency installation (when defined), and many usability enhancements and fixes. * New /Bedgraph-to-bigwig/ <http://wiki.galaxyproject.org/Learn/Datatypes#BedGraph> tool plus /Filter/ tool updated. * /Workflows/ now include option to export an image and the core /Framework/ now allows more unified reference genome usage and access. * /Ten Community Pull-Requests/ incorporated, plus another contribution to the tool Shed, addressing general usability, API, tools, error handling, workflows, and more. Thanks!! * Review highlights from the latest monthly */Galaxy Update/* <http://wiki.galaxyproject.org/GalaxyUpdates> newsletter and Galaxy Project Stats <http://wiki.galaxyproject.org/Galaxy%20Project/Statistics>! * Plus bug fixes and related enhancements for visualizations, histories, workflows, and tools. *http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* *http://galaxy-dist.readthedocs.org * new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull $ hg update release_2013.02.08 To ensure that you continue to receive updates about *Galaxy Distributions and News Briefs* <http://wiki.galaxyproject.org/DevNewsBriefs>, be sure to subscribe to the Galaxy-Announce mailing list <http://wiki.galaxyproject.org/MailingLists#The_lists>, a low-volume list dedicated to News Items <http://wiki.galaxyproject.org/News> and priority messages from the Galaxy community <http://wiki.galaxyproject.org/Community> and project core team <http://wiki.galaxyproject.org/Galaxy%20Project>. /Thanks for using Galaxy,/ The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>

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February 2013 Galaxy Update
by Dave Clements 01 Feb '13

01 Feb '13

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2013 Galaxy Community Conference (GCC2013) Training Day: Please vote!
by Dave Clements 28 Jan '13

28 Jan '13

Hello all, A list of possible topics <http://bit.ly/gcc2013td> for the GCC2013 Training Day <http://bit.ly/gcc2013td> is now available at http://bit.ly/gcc2013td. Please take a few minutes to review these possibilities <http://bit.ly/gcc2013td> and *then vote for your three favorite topics* at http://bit.ly/gcc2013tdpoll* Your votes will determine not only the topics that are offered, but also which topics should be offered more than once, assigned to the larger rooms, and which ones should not be scheduled at the same time. Your vote matters. Once voting closes on 11 February, we will contact possible instructors and publish a Training Day schedule before registration opens on 22 February. *About the GCC2013 Training Day* The 2013 Galaxy Community Conference (GCC2013)<http://galaxyproject.org/GCC2013> will start on 30 June with a Training Day <http://bit.ly/gcc2013td> featuring 4 parallel tracks, each with three workshops, each of which are two 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, and hope to see you in Oslo! Dave Clements, on behalf of the GCC2013 Organizing Committee * Note: You don't have to vote for exactly three topics. You can vote for fewer topics and have each vote count for more, or you can vote for more topics and have each vote count for less. Links: http://bit.ly/gcc2013td - Training Day possible topics list http://bit.ly/gcc2013tdpoll - Vote! http://galaxyproject.org/GCC2013 - Conference home page http://bit.ly/gcc2013prom - help get the word out -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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GalaxyAdmins Meetup -- January 16 at 10 AM Central
by IIHG Galaxy Administrator 14 Jan '13

14 Jan '13

Hello, The next GalaxyAdmins Meetup will be Wednesday, January 16, 2013 from 10 AM to 11 AM US Central time. John Chilton of the Minnesota Supercomputing Institute will cover "Deploying Production Galaxy Environments on OpenStack with CloudBioLinux and CloudMan". You can join the meetup at https://globalcampus.uiowa.edu/join_meeting.html?meetingId=1262341808106. We use the Blackboard Collaborate Web Conferencing system for the meetup. Downloading the required applets in advance and using a headphone with microphone to prevent audio feedback during the call is recommended. Thank you. -- Srinivas Maddhi Senior Systems Administrator Iowa Institute for Human Genetics The University of Iowa

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Galaxy January 11, 2013 Distribution & News Brief
by Jennifer Jackson 11 Jan '13

11 Jan '13

*Galaxy January 11, 2013 Distribution & News Brief* <http://wiki.galaxyproject.org/News/2013_01_11_DistributionNewsBrief> * Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11>* * Highlights:* * /*GCC2013 Training Day Topic Nomination closes TODAY!*/ Read more... <http://wiki.galaxyproject.org/News/GCC2013TrainingDayNominations> or see http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay * XML defined Tool shed repository dependencies <http://wiki.galaxyproject.org/DefiningRepositoryDependencies> introduced * Various enhancements <http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11#Other_Tool_Shed> to Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed> containers, display of README files and SVG images, and the tool shed's functional test framework <http://wiki.galaxyproject.org/HostingALocalToolShed#Functional_test_framewo…>. * New genomes <http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11#Data> added to *Main <http://wiki.galaxyproject.org/Main>* Galaxy instance and rsync download. * Plus bug fixes and related enhancements for visualizations, histories, workflows, and tools. * http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* *http://galaxy-dist.readthedocs.org* new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r a4113cc1cb5e / *Thanks for using Galaxy,* / The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team> -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Nominate topics for the 2013 Galaxy Community Conference (GCC2013) Training Day
by Dave Clements 07 Jan '13

07 Jan '13

Hello all, Nominations are now open <http://bit.ly/gcc2013nom> for Training Day topics<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay>at the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013>. GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions. Any topic of interest to the Galaxy Community can be nominated<http://bit.ly/gcc2013nom>(see what was offered at GCC2012<http://wiki.galaxyproject.org/Events/GCC2012/TrainingDay>). Topics can be repeats from last year or brand new, and you are encouraged to nominate as many topics as you like. The 2013 Galaxy Community Conference (GCC2013) <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions. Nominations will be compiled into a uniform list, and then topics will be voted on by the Galaxy Community starting in late January. Topic nomination closes 11 January. Thanks, Dave Clements, on behalf of the GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers#Organizing_Committee> Links: http://bit.ly/gcc2013nom - nominate a topic http://bit.ly/gcc2013td - Training Day page http://galaxyproject.org/GCC2013 - Conference home page http://bit.ly/gcc2013prom - help get the word out -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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January 2013 Galaxy Update
by Dave Clements 02 Jan '13

02 Jan '13

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Galaxy December 20, 2012 Distribution & News Brief
by Jennifer Jackson 20 Dec '12

20 Dec '12

*Galaxy Dec 20, 2012 Distribution & News Brief <http://wiki.galaxyproject.org/News/2012_12_20_DistributionNewsBrief>* *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_20>* *Highlights:* * *Required Metadata Reset* for instances running *Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed>* repositories. Be sure to *learn how <http://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories>*. * *Simplified tool config*: all tools (including tool shed repos) can now have handlers and runners assigned based on their "short id". * *New* GFF <http://wiki.galaxyproject.org/Learn/Datatypes#GFF>/GFF3 <http://wiki.galaxyproject.org/Learn/Datatypes#GFF3> annotation support for *Cuffcompare/merge/diff <http://cufflinks.cbcb.umd.edu/manual.html>*. * *More Updated* tools: *TopHat2 <http://tophat.cbcb.umd.edu/manual.html>*, *Bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml>*. * *Multiple pull-requests* contributed by community (thanks!): *#83 <https://bitbucket.org/galaxy/galaxy-central/pull-request/83/allow-a-datatyp…>*, *#85 <https://bitbucket.org/galaxy/galaxy-central/pull-request/85/another-round-o…>*, *#90 <https://bitbucket.org/galaxy/galaxy-central/pull-request/90/patch-to-make-e…>*, *#91* <https://bitbucket.org/galaxy/galaxy-central/pull-request/91/fixing-missing-…>. * *Issue tracking help* is now covered in detailed in our new wiki: *Using the Galaxy Issue Board <http://wiki.galaxyproject.org/Issues>* * *GCC2013 Training Day Topic Nominations <http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> are now open* through /*January 11th*/ <http://wiki.galaxyproject.org/Events/GCC2013/KeyDates> * *Plus* more *Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed>* updates, *Bug Fixes*, and improvements to *Trackster, UI, Libraries, and Histories*. * getgalaxy.org <http://getgalaxy.org>* *bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* *galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org> * new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r 36ad8aa7b922 *Best wishes for a safe and happy holiday*, /*The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>*/ -- Jennifer Jackson http://galaxyproject.org

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December 3, 2012 Distribution & News Brief
by Jennifer Jackson 03 Dec '12

03 Dec '12

December 3, 2012 Distribution & News Brief <http://wiki.galaxyproject.org/News/2012_12_03_DistributionNewsBrief> * Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_03>* * Highlights:* * *NGS: Mapping* tools *Bowtie <http://bowtie-bio.sourceforge.net/index.shtml>* and *Lastz <http://www.bx.psu.edu/%7Ersharris/lastz/>* have moved from the *Galaxy distribution <https://bitbucket.org/galaxy/galaxy-dist>* to the *Galaxy Main Tool Shed <http://toolshed.g2.bx.psu.edu/>*. * Improvements in the display of *Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed>* repository dependencies and contents. * More *Tool Shed <http://toolshed.g2.bx.psu.edu/>* updates including details of the Functional test framework <http://wiki.galaxyproject.org/HostingALocalToolShed#Functional_test_framewo…>, a new hgweb.config file and HgWebConfigManager tool, plus other management features. * Updated *UI* display and functionality for datasets and histories: new *paused* state and "resume/paused" toggle, new *History menu options*, and improved *Scatterplot* visualizations. * The *SGE* job runner has now been fully deprecated and replaced with *DRMAA*. * Several enhancements to aid with *reproducibility*: "Re-run" and "Extract workflow" validates datasets and tools, respectively, and a new data tables registry within the Administration menu, along with associated tools, corrects or warns about tool migration issues. * Highlights from the new Galaxy *CloudMan <http://usegalaxy.org/cloud>* release and /*December 2012 Galaxy Update <http://wiki.galaxyproject.org/GalaxyUpdates/2012_12>*/. * http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* *http://galaxy-dist.readthedocs.org* new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r f364d992270c * Thanks for using Galaxy!* The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team> -- Jennifer Jackson http://galaxyproject.org

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