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March 12, 2012 Galaxy Development News Brief
by Jennifer Jackson 12 Mar '12

12 Mar '12

Dear Galaxy Community, The latest Galaxy distributionhas been released: March 12, 2012 Galaxy Development News Brief <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_03_12> *Mercurial pull:* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 40f1816d6857 Important Upcoming Changes to Tool Organization: The _*Emboss tools and Emboss datatypes will be eliminated from the Galaxy distribution in the NEXT release*_. Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised *"Migrating tools"* <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…> section of the Galaxy tool shed wiki to understand how this process will work: Migrating tools from the Galaxy distribution to the Galaxy Main tool shed <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…> (Summary) In 2012, the Galaxy development team will begin the process of migrating the tools that are currently available in the Galaxy distribution to the Galaxy Main tool shed. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. Read more... <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…> Release Highlights: * Galaxy toolsXML configuration <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…>, managing tool panel layout <http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_to…>, and Galaxy tool versions <http://wiki.g2.bx.psu.edu/Tool%20Shed#Galaxy_Tool_Versions>. * RNA-Seq Tools: Added CuffMerge <http://cufflinks.cbcb.umd.edu/>version 1.0.0, Updated TopHat <http://tophat.cbcb.umd.edu/>default parameters * External Display Apps: Added *RViewer* <http://rviewer.lbl.gov/rviewer>, Updated *IGV * <http://www.broadinstitute.org/igv/> * Visualize *ENCODE* <http://genome.ucsc.edu/ENCODE> "peak" datatype tracks in the Galaxy Track Browser(aka Trackster) * Multiple Workflowupdates including enhancements to/input dataset options, display modes, and sharing * *CloudMan* <http://wiki.g2.bx.psu.edu/Admin/Cloud> now offers /preliminary support for OpenNebula cloud type <http://bitbucket.org/galaxy/cloudman/src/tip/cm/clouds/opennebula.py>/ and a larger /default tools volume/ 10GB vs old 2GB). *Need help with a local instance? * Installation and Admin Instructions: http://getgalaxy.org Searchwith our custom google tools: * All Galaxy mailings lists <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>for prior Q & A * Information about deploying, developing, customizing, and administering <http://galaxyproject.org/search/getgalaxy> Galaxy * Information about using <http://galaxyproject.org/search/usegalaxy> Galaxy Consider *subscribing to the galaxy-dev* <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing> mailing list Thanks for using Galaxy, The Galaxy team ------- http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki

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March 12, 2012 Galaxy Development News Brief
by Jennifer Jackson 12 Mar '12

12 Mar '12

Dear Galaxy Community, The latest *Galaxy distribution* has been released: March 12, 2012 Galaxy Development News Brief <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_03_12>. *Mercurial pull:* new: % hg clone http://www.bx.psu.edu/hg/galaxygalaxy-dist upgrade: % hg pull -u -r 40f1816d6857 *Important Upcoming Changes to Tool Organization*: The _*Emboss tools and Emboss datatypes**will be eliminated from the Galaxy distribution in the NEXT release*_. Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised*"Migrating tools" <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…>*<http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…>section of the Galaxy tool shed wiki to understand how this process will work: Migrating tools from the Galaxy distribution to the Galaxy Main tool shed <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…> (Summary) In 2012, the Galaxy development team will begin the process of migrating the tools that are currently available in the Galaxy distribution to the Galaxy Main tool shed. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. Read more... <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…> *Release Highlights*: * *Galaxy tools* XML configuration <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…>, managing tool panel layout <http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_to…>, and Galaxy tool versions <http://wiki.g2.bx.psu.edu/Tool%20Shed#Galaxy_Tool_Versions>. * *RNA-Seq Tools*: Added *CuffMerge* <http://cufflinks.cbcb.umd.edu/> version 1.0.0, Updated *TopHat* <http://tophat.cbcb.umd.edu/> default parameters * *External Display Apps*: Added *RViewer <http://rviewer.lbl.gov/rviewer>*, Updated *IGV <http://www.broadinstitute.org/igv/>* * *Visualize *ENCODE <http://genome.ucsc.edu/ENCODE/> "peak" datatype tracks in the *Galaxy Track Browser* (aka Trackster) * Multiple *Workflow* updates including enhancements to/input dataset options, display modes, and sharing/. * *CloudMan <http://wiki.g2.bx.psu.edu/Admin/Cloud>* now offers /preliminary support for OpenNebula cloud type <https://bitbucket.org/galaxy/cloudman/src/tip/cm/clouds/opennebula.py>/ and a /larger default tools volume /(10GB vs old 2GB). *Need help with a local instance? * *Installation and Admin Instructions*: http://getgalaxy.org *Search* with our custom google tools: * All Galaxy mailings lists <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching> for prior Q & A * Information about deploying, developing, customizing, and administering Galax <http://galaxyproject.org/search/getgalaxy>y * Information about using Galaxy <http://galaxyproject.org/search/usegalaxy> *Consider****subscribing to the galaxy-dev *mailing list <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing> Thanks for using Galaxy, The Galaxy team ------- http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki

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March 2012 Galaxy Update
by Dave Clements 29 Feb '12

29 Feb '12

Hello all, The March 2012 Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02>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 * complements the *Galaxy Development News Briefs<http://wiki.g2.bx.psu.edu/DevNewsBriefs> * which accompany new Galaxy releases and focus on Galaxy code updates. *Highlights:* - 28 New Papers<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#New_Papers> - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Who.27s_Hiring>at four different institutions - Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Upcoming_Events_and_Deadlin…> - GCC2012 Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#GCC2012_Update>, including - Abstract submission is open. - Training Day topics are set. - Tool Shed Contributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_03#Tool_Shed_Contributions> If you have anything you would like to see in the April *Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates> *, please let me know. Thanks, Dave C. -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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2012 Galaxy Community Conference (GCC2012): Now Accepting Abstracts
by Dave Clements 13 Feb '12

13 Feb '12

Hello all, Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> are now being accepted for oral presentations at the 2012 Galaxy Community Conference (GCC2012) <http://wiki.g2.bx.psu.edu/Events/GCC2012>. Submissions on any topics of interest to the Galaxy community are encouraged. Areas of interest include, but are not limited to: - Best practices for local Galaxy installation and management - Integrating tools and/or data sources into the Galaxy framework - Deploying galaxy on different infrastructures - Compelling or novel uses of Galaxy for biomedical analysis See the GCC2011 program <http://wiki.g2.bx.psu.edu/Events/GCC2011> for an idea of the breadth of topics that can be covered. Oral presentations will be approximately 15-20 minutes long, including time for question and answer. There will also be an opportunity for lightning talks, which will be solicited at the meeting. The submission deadline is April 16. See the GCC2012 Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> page for more details and how to submit. GCC2012 <http://wiki.g2.bx.psu.edu/Events/GCC2012> will be held, July 25-27 in Chicago, Illinois, United States. The main meeting will run for two full days <http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>, and be preceded by a full day of training workshops<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>. If you are a bioinformatics tool developer, data provider, workflow developer, power bioinformatics user, sequencing or bioinformatics core staff, or a data and analysis archival specialist, then GCC2012 is relevant to you. Registration will open in March. GCC2012 is hosted by the University of Illinois at Chicago <http://uic.edu/>, the University of Illinois at Urbana-Champaign <http://illinois.edu/>, and the Computation Institute <http://www.ci.anl.gov/>. Links: http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/Events/GCC2012/Abstracts Thanks, Dave Clements -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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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 27 Jan '12

27 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 06 Jan '12

06 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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