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February 2012 Galaxy Update
by Dave Clements 31 Jan '12

31 Jan '12

Hello all, The inaugural edition <http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02> of *Galaxy Update <http://wiki.g2.bx.psu.edu/GalaxyUpdates>* is now available. *Galaxy Update <http://wiki.g2.bx.psu.edu/GalaxyUpdates>* is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates* will complement the *Galaxy Development News Briefs<http://wiki.g2.bx.psu.edu/DevNewsBriefs> * which accompany new Galaxy releases and focus on Galaxy code updates. *Highlights:* - New Papers <http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#New_Papers> - New Public Server: MGTAXA<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#New_Public_Server:_MGTAXA> - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#Who.27s_Hiring> - Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#Upcoming_Events_and_Deadlin…> - GCC2012 Sponsors<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#GCC2012_Sponsors> - New Distributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#New_Distributions> If you have anything you would like to see in the March *Galaxy Update*, please let me know. Dave Clements Link: http://galaxyproject.org/wiki/GalaxyUpdates/2012_02 -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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January 27, 2012 Galaxy Distribution & News Brief
by Jennifer Jackson 28 Jan '12

28 Jan '12

January 27, 2012 Galaxy Distribution & News Brief Complete News Brief * http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_01_27 Highlights: * Important metadata and Python 2.5 support corrections * SAMtools upgraded for version 0.1.18. Mpileup added. * Dynamic filtering, easy color options, and quicker indexing enhance Trackster * Set up your Galaxy instance to run cluster jobs as the real user, not the Galaxy owner * Improvements to metadata handling and searching in the Tool Shed * Improved solutions for schema access, jobs management, & workflow imports and inputs. * New datatypes (Eland, XML), multiple tool enhancements, and bug fixes. Get Galaxy! * http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 26920e20157f Read the release announcement and see the prior release history * http://wiki.g2.bx.psu.edu/DevNewsBriefs/ Need help with a local instance? Search with our custom google tools! * http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching And consider subscribing to the galaxy-dev mailing list! * http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing -- Jennifer Jackson Galaxy Team http://usegalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki/Support

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January 20, 2012 Galaxy Development News Brief
by Jennifer Jackson 20 Jan '12

20 Jan '12

January 20, 2012 Galaxy Development News Brief Highlights: * New Object Store data integration layer introduced * RNA-seq updates: TopHat to 1.4.0 and Cufflinks, CuffDiff, CuffCompare to 1.3.0. * Tool Shed installation features and community tool additions * Trackster performance upgrades and new drag & drop composite track creation Mercurial pull: hg pull -u -r 63bc46cc73b7 Complete News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_01_20 Release history http://wiki.g2.bx.psu.edu/DevNewsBriefs/ Install/Administration Help http://getgalaxy.org Support http://galaxyproject.org/wiki/Support Thanks for using Galaxy!

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Galaxy @ PAG 2012
by Dave Clements 07 Jan '12

07 Jan '12

Hello all, Plant and Animal Genome XX (PAG2012) starts in San Diego on January 14. If you are attending PAG then you will have (at least) a half-dozen opportunities to learn more about Galaxy and how it is being used to support research. There will be workshops introducing Galaxy, and on deploying Galaxy in the cloud, and talks and posters on using Galaxy and several local Galaxy deployments. See the Galaxy @ PAG2012 page (http://wiki.g2.bx.psu.edu/Events/PAG2012) and the conference website (http://www.intlpag.org/) for more information. Dannon Baker and Dave Clements from the Galaxy Team ( http://wiki.g2.bx.psu.edu/Galaxy%20Team) will also be there throughout the meeting. Please feel free to ask us questions, or just introduce yourself. Hope to see you in San Diego, Dave Clements and Dannon Baker -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Search the Galaxy!
by Dave Clements 20 Dec '11

20 Dec '11

Hello all, I am happy to announce that Galaxy now has several Google Custom Searches that make it much easier (really - way, way easier) to find answers to your questions about Galaxy. They are available at http://galaxyproject.org/search/. *Name & URL * * Description * ** *Galaxy Web Search <http://galaxyproject.org/search/web>* http://galaxyproject.org/search/web Searches *everything:* Galaxy Main <http://wiki.g2.bx.psu.edu/Main>, the mailing list archives <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>, the Galaxy wiki <http://wiki.g2.bx.psu.edu/FrontPage>, Galaxy's source code at Bitbucket <https://bitbucket.org/galaxy/galaxy-central/src/tip/>, and the Tool Shed <http://wiki.g2.bx.psu.edu/Tool%20Shed>. The results are returned in a unified list, and are also grouped into several categories. *Galaxy Mailing List Search <http://galaxyproject.org/search/mailinglists>* http://galaxyproject.org/search/mailinglists Searches all the Galaxy mailing list archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>. The results are returned in a unified list, and are also grouped by mailing list.** *UseGalaxy Search <http://galaxyproject.org/search/usegalaxy>* http://galaxyproject.org/search/usegalaxy Search for information about *using* Galaxy. Searches Galaxy Main<http://wiki.g2.bx.psu.edu/Main>( UseGalaxy.org <http://usegalaxy.org/>), the wiki<http://wiki.g2.bx.psu.edu/Learn>(excluding the Admin <http://wiki.g2.bx.psu.edu/Admin> pages), and the Galaxy-User and Galaxy-Announce mailing list archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>. *GetGalaxy Search <http://galaxyproject.org/search/getgalaxy>* http://galaxyproject.org/search/getgalaxy Search for information about installing, customizing, and developing Galaxy. Searches the Galaxy Bitbucket (source) site<https://bitbucket.org/galaxy/galaxy-central/src/tip/>, the Tool Shed <http://toolshed.g2.bx.psu.edu/>, the wiki<http://wiki.g2.bx.psu.edu/Admin>(excluding the Learn <http://wiki.g2.bx.psu.edu/Learn> pages), and the Galaxy-Dev and Galaxy-Announce mailing list archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>. We strongly encourage you to give these try. Please send feedback and suggestions to Galaxy Outreach <outreach(a)galaxyproject.org>. Happy searching (and a Happy New Year!), Dave Clements -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Looking for Galaxy related papers (or have written one)? There is a new Galaxy Group @ CiteULike
by Dave Clements 14 Dec '11

14 Dec '11

Hello all, A new Galaxy Group <http://www.citeulike.org/group/16008/order/group_rating>has been created at the CiteULike <http://citeulike.org/> social bookmarking service to organize papers that are about, use, or reference Galaxy. The Galaxy Group<http://www.citeulike.org/group/16008/order/group_rating>is open to any CiteULike user (and anyone can become a CiteULike user). Group members can add papers to the group, assign tags, and rate papers. CiteULike makes extensive use of *tags* to organize and categorize papers. The Galaxy group uses this set of tags<http://wiki.g2.bx.psu.edu/CiteULike#CiteULike_Tags>to categorize papers. If you want to help other Galaxy users and sites find papers that are relevant to them, or help the Galaxy Project keep track of what papers (and communities) are using Gaalxy, then please help by adding relevant papers to the Galaxy Group Library<http://www.citeulike.org/group/16008/order/group_rating>and/or rating and tagging the papers that are there. *We particularly need help with papers that were published before this year, as very few of them are in the initial list. * Links: http:/galaxyproject.org/wiki/CiteULike - Explanation of tags http://www.citeulike.org/group/16008/order/group_rating - Galaxy Group list of papers Thanks, Dave Clements PS: To cite the Galaxy Project, see http://galaxyproject.org/wiki/Citing%20Galaxy. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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January 2012 Galaxy Events: Dec 15 Deadline for Czech Republic Workshop
by Dave Clements 08 Dec '11

08 Dec '11

Hello all, The January Events <http://wiki.g2.bx.psu.edu/Events> email is going out a little early this month, mainly because of a *December 15 deadline for the Galaxy Developer Workshop in the Czech Republic<http://evomics.org/workshops/galaxy-developer-workshop/> *. There are Galaxy-related events on (at least) 3 continents next month: * Date * * Topic/Event * * Venue/Location * * Contact * January 8-21 *2012 Workshop on Genomics<http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-kruml…> * Features Galaxy and much more. Český Krumlov, Czech Republic James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 14-18 *Galaxy Session<http://pag.confex.com/pag/xx/webprogrampreliminary/Paper2350.html>@ GMOD Workshop<http://pag.confex.com/pag/xx/webprogrampreliminary/Session1123.html> *, and *The Galaxy Platform: Running Analyses in the Cloud<http://pag.confex.com/pag/xx/webprogrampreliminary/Paper4623.html>@ Cloud Computing Session<http://pag.confex.com/pag/xx/webprogrampreliminary/Session1139.html> * PAG 2012 <http://wiki.g2.bx.psu.edu/Events/PAG2012>, San Diego, California, United States Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements> Dannon Baker January 17 *Reproducible workflows for next generation sequencing analysis<http://www.nowgen.org.uk/facilities/events/event.php?id=30> * Nowgen <http://www.nowgen.org.uk/>, University of Manchester<http://www.manchester.ac.uk/>, United Kingdom Tom Hancocks <training(a)nowgen.org.uk> January 23 *Galaxy Developer Workshop<http://evomics.org/workshops/galaxy-developer-workshop/> Application deadline is December 15.* Český Krumlov, Czech Republic <http://www.ckrumlov.info/php/>, immediately following the Workshop on Genomics<http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-kruml…>, (which also features Galaxy content) James Taylor <http://wiki.g2.bx.psu.edu/JamesTaylor> January 26 *今回の講習会では，「Next-Generation Sequencer(NGS) 微生物解析と Galaxy ツール」を中心に講義と実習を行ないます。講義内容をよりよく理解して頂くために，PC を使用した実習を行ないます。<http://www.ddbj.nig.ac.jp/ddbjing/ddbjing.html#DDBJ> * (Next-Generation Sequencing (NGS) and microbiological analysis with Galaxy) DNA Data Bank of Japan (DDBJ), National Institute of Genetics<http://www.ddbj.nig.ac.jp/> DDBJ <http://www.ddbj.nig.ac.jp/addresses-j.html> And I apologize in advance if I messed up the translation of the event at DDBJ <http://www.ddbj.nig.ac.jp/ddbjing/ddbjing.html#DDBJ>! Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Galaxy-Announce: A new, moderated, low-volume Galaxy Mailing List
by Dave Clements 02 Dec '11

02 Dec '11

Hello all, There is a new mailing list in the Galaxy: Galaxy-Announce. Galaxy-Announce is a *moderated, low-volume *mailing list. Galaxy-Announce complements the existing Galaxy-User (about the public server at UseGalaxy.org) and Galaxy-Dev (deployment and development) mailing lists. However, unlike those relatively high-volume mailing lists, Galaxy-Announce will only have a few messages each month. If you are looking for a Galaxy list that just covers the big stuff, this is your list. To subscribe to the list please add your email address to the list here: http://lists.bx.psu.edu/listinfo/galaxy-announce See http://wiki.g2.bx.psu.edu/Mailing%20Lists for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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