March 2012 - galaxy-announce - lists.galaxyproject.org

2012 Galaxy Community Conference (GCC2012) Early Registration is Now Open
by Dave Clements 20 Mar '12

20 Mar '12

Hello all, We are pleased to announce that early registration<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register>for the 2012 Galaxy Community Conference (GCC2012)<http://wiki.g2.bx.psu.edu/Events/GCC2012>is now open. GCC2012 will be held July 25-27, at the UIC Forum <http://www.uic.edu/depts/uicforum/>, in Chicago, Illinois. The conference will feature two full days<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>of presentations, discussions, lightning talks, and breakouts. We have also added a new full day of training<http://wiki.g2.bx.psu.edu/Events/GCC2012/TrainingDay>this year, featuring 3 parallel tracks with four workshops each, covering seven different topics. The Galaxy Community Conference is for: - Sequencing core facility staff - Bioinformatics core staff - Bioinformatics tool and workflow developers - Bioinformatics focused principal investigators and researchers - Data producers - Power bioinformatics users This event will help you with integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. GCC2012 is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology. Registration <http://wiki.g2.bx.psu.edu/Events/GCC2012/Register> is very affordable, especially for post-docs and students. You can can save an additional 40% by registering on or before June 11. Conference lodging<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodging>can also be booked. Low-cost rooms have been reserved on the UIC campus<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#James_Stuckel_Towers>. You can also stay at the official conference hotel<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Crowne_Plaza_Chicago_Met…>, at a substantial discount arranged for conference attendees. There are a limited rooms available in both, and you are encouraged to register early<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register>, if you would like to take advantage of these. Abstract submission <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> is also open, from now through April 16. Abstract submissions<http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts>on any topic of interest to the Galaxy community are strongly encouraged. See the Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> page for details. Please let me know if you have any questions (or just talk to me at the April 2012 GMOD Meeting). Looking forward to seeing you in Chicago this July! Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements>, on behalf of the GCC2012 Organizing Committee<http://wiki.g2.bx.psu.edu/Events/GCC2012/Organizing%20Committee> PS: Please help get the word out! A flyer and graphics are at http://wiki.g2.bx.psu.edu/Events/GCC2012/Promotion. -- 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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GCC2012 Early Registration is Now Open
by Dave Clements 20 Mar '12

20 Mar '12

Hello all, We are pleased to announce that early registration<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register>for the 2012 Galaxy Community Conference (GCC2012)<http://wiki.g2.bx.psu.edu/Events/GCC2012>is now open. GCC2012 will be held July 25-27, at the UIC Forum <http://www.uic.edu/depts/uicforum/>, in Chicago, Illinois. The conference will feature two full days<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>of presentations, discussions, lightning talks, and breakouts. We have also added a new full day of training<http://wiki.g2.bx.psu.edu/Events/GCC2012/TrainingDay>this year, featuring 3 parallel tracks with four workshops each, covering seven different topics. The Galaxy Community Conference is for: - Sequencing core facility staff - Bioinformatics core staff - Bioinformatics tool and workflow developers - Bioinformatics focused principal investigators and researchers - Data producers - Power bioinformatics users This event will help you with integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. GCC2012 is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology. Registration <http://wiki.g2.bx.psu.edu/Events/GCC2012/Register> is very affordable this year, especially for post-docs and students. You can can save an additional 40% by registering on or before June 11. Conference lodging<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodging>can also be booked. Low-cost rooms have been reserved on the UIC campus<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#James_Stuckel_Towers>. You can also stay at the official conference hotel<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Crowne_Plaza_Chicago_Met…>, at a substantial discount arranged for conference attendees. There are a limited rooms available in both, and you are encouraged to register early<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register>, if you would like to stay in either. Finally, abstract submission<http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts>is also open, from now through April 16. Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> on any topic of interest to the Galaxy community are strongly encouraged. See the Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> page for details. Looking forward to seeing you in Chicago! Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements>, on behalf of the GCC2012 Organizing Committee<http://wiki.g2.bx.psu.edu/Events/GCC2012/Organizing%20Committee> PS: Please help get the word out! A flyer and graphics are at http://wiki.g2.bx.psu.edu/Events/GCC2012/Promotion -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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March 12, 2012 Galaxy Development News Brief
by Jennifer Jackson 13 Mar '12

13 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/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 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 <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 * *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 <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 13 Mar '12

13 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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