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Galaxy September 7, 2012 Distribution & News Brief
by Jennifer Jackson 07 Sep '12

07 Sep '12

*Galaxy September 7, 2012 Distribution & News Brief* http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_07 /*Highlights:*/ * *NCBI BLAST+ has moved* from the Galaxy distribution to the Galaxy's Main Tool Shed. * *Tool Shed* *is now running Mercurial version 2.2.3*. Many updates and refinements including UI/metadata changes - read the full report. * *Streamline local setup* with the *Reference Genome rsync Server*: same builds and indexes as on the public Galaxy Main instance. * More *updates to* *Output and Error Handling* including updated documentation and enhancements to exit code checks. * *TopHat2 / Bowtie2* latest support includes Tophat2 fusions output, Bowtie2 sorted BAMs, and a new RNA-seq Tutorial. * *Trackster* updates include improved *support for* *bigWig / bigBed*, new support for *bedGraph*, and a new *search feature for GFF / GTF / BED* datasets. * Plus many *other* *Workflow, API, Source, UI* *features* and a summary of *recent Galaxy Update* highlights. http://getgalaxy.org http://bitbucket.org/galaxy/galaxy-dist *new: * $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist *upgrade:* $ hg pull -u -r e6444e7a1685 * * *Thanks for using Galaxy!* Jennifer Jackson & Galaxy Team -- http://galaxyproject.org http://usegalaxy.org

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September 2012 Galaxy Update
by Dave Clements 29 Aug '12

29 Aug '12

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Galaxy-France -- Communauté française de Galaxy (French Galaxy Community)
by Dave Clements 27 Aug '12

27 Aug '12

Bonjour à tous, Avec l'aide et le soutien de l'équipe Galaxy, nous venons de mettre en ligne la liste de diffusion Galaxy France. Cette liste a pour but de partager et communiquer sur nos différentes expériences avec Galaxy au sein de l'hexagone. La langue officielle de cette liste est le français. Vous avez besoin d'aide dans l'utilisation de Galaxy, Vous hébergez un serveur public Galaxy, Vous maintenez une instance locale de Galaxy, Vous venez de déposer un outil sur le toolshed, Vous avez des trucs et astuces pouvant interresser la communauté, Vous organisez des formations avec Galaxy, Rejoignez nous en vous inscrivant à http://lists.bx.psu.edu/listinfo/galaxy-france Les archives de cette liste sont disponibles à http://france.list.galaxyproject.org A très bientôt sur la liste Galaxy France, Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer Jackson ------------------------------ --------------------- Hi everyone, With the help and the support of the Galaxy team, we just put online the Galaxy French mailing list. The aim of this list is to share and communicate on our different experiences with Galaxy in France. * The main language is French. * Topics include, but are not limited to: You need help in the use of Galaxy, You're hosting a Galaxy public server, You're maintaining a local instance of Galaxy, You just add a new tool on the toolshed, You have some tips that could interested the community, You organize workshops with Galaxy, Join us by subscribing at http://lists.bx.psu.edu/listinfo/galaxy-france The list's archives are also available at http://france.list.galaxyproject.org See you soon on the Galaxy-France list, The administrators: Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer Jackson -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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August 2012 Galaxy Update
by Dave Clements 31 Jul '12

31 Jul '12

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Galaxy July 20, 2012 Distribution & News Brief
by Jennifer Jackson 21 Jul '12

21 Jul '12

Galaxy July 20, 2012 Distribution & News Brief *Complete News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_07_20* *Highlights: http://wiki.g2.bx.psu.edu/News/Jul202012%20Distribution%20News%20Brief* * *Freebayes *has moved from the /Galaxy distribution to the Galaxy's Main Tool Shed/ * *EMBOSS* version 5.0.0 tool dependencies in the emboss_5 repository of the Galaxy Main Tool Shed updated to include information for automatically installing. * *Tool Shed* now also supports specifying the third party tool dependencies to be automatically installed in new repositories * *Admin Genome Indexing* is now in /BETA/. Download, index, and track progress right from the admin UI! * *Improved Error Handling* that captures EXIT codes, STDOUT, and STDERR from tools in XML. Be sure to read full details. * *TopHat2/Bowtie2* latest support includes option to 'report discordant pairs', updated tests, and more preset options. * *Trackster* new parameter space visualization. /Includes BRAND NEW Features!!/ More details coming soon, but give a test drive now. *http://getgalaxy.org* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r ec29ce8e27a1 *Thanks for using Galaxy!* We hope to see everyone in /Chicago/ @ *GCC2012*!! The Galaxy Team

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GCC2012 Registration Deadline
by Dave Clements 17 Jul '12

17 Jul '12

Hello all, This is the final email reminder that the registration deadline for the 2012 Galaxy Community Conference, is at Midnight, Central US time, on Wednesday, July 18. If you aren't registered by the end of Wednesday, you will pay *double* using late/on-site registration. The deadline for booking hotel rooms at the discounted rate has been extended until July 23, or until they fill up (and it looks like they will fill up). The 2012 conference already has more content and more participants than any previous Galaxy meeting. We would love to have you join us. See http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> for details and links. 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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July 2012 Galaxy Update
by Dave Clements 28 Jun '12

28 Jun '12

Hello all, The July 2012 Galaxy Update is now available<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07>. *Highlights:* - GCC2012 is July 25-27!<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#GCC2012_is_July_25-27.21> - Register by July 18<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register> - Other Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Upcoming_Events_and_Deadlin…> ,* including these deadlines in the next several days* - Galaxy Workshops in South Africa<http://wiki.g2.bx.psu.edu/News/GalaxyWorkshopsInSouthAfrica>(deadline: *June 30*) and the South African Genetics & Bioinformatics Society Conference <http://genetics.cmc-uct.co.za/> (deadline *July 1*) - Systems Bioinformatics Workshop<http://gaggle.systemsbiology.net/workshop2012/>(deadline: *June 30*) - GMOD Summer School<http://gmod.org/wiki/2012%20GMOD%20Summer%20School>(deadline: *July 9*) - 31 New Papers<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#New_Papers>, including two new *Current Protocols* - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Who.27s_Hiring>at six different institutions - Tool Shed Contributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Tool_Shed_Contributions> - A new CloudMan distribution was released last month<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#New_Distributions> - Plus <http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Other_News> - Easily wrap your R functions as Galaxy tools - help schedule the first GalaxyCzars<http://wiki.g2.bx.psu.edu/Community/GalaxyCzars>conference call on July 9 or 10 - and lots of new screencasts, tutorials, and new genomes on main If you have anything you would like to see in the August *Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates> *, please let me know. Thanks, Dave Clements -- 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 ENDS THIS MONDAY JUNE 11
by Dave Clements 10 Jun '12

10 Jun '12

Hello all, Just a *final* reminder that early registration for the 2012 Galaxy Community Conference (GCC2012)<http://galaxyproject.org/wiki/Events/GCC2012> *closes on Monday June 11 (*which is probably* today* when you read this*)*. Registering early saves 36 to 42% on registration costs, and allows you to sign up for the GCC2012 Training Day<http://galaxyproject.org/wiki/Events/GCC2012/TrainingDay>and book discounted conference lodging<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodging> *before they fill up*. *Register today <http://wiki.g2.bx.psu.edu/Events/GCC2012/Register>. * GCC2012 <http://galaxyproject.org/wiki/Events/GCC2012> will be held July 25-27, in Chicago, Illinois, United States. This year GCC2012 features a full day of tutorial sessions<http://galaxyproject.org/wiki/Events/GCC2012/TrainingDay>with 3 parallel tracks, each featuring four, 90 minute workshops and covering 10 different topic, including the newly added Variant and SNP Analsys, RNA-Seq Analysis, and Galaxy Code Architecture sessions<http://wiki.g2.bx.psu.edu/Events/GCC2012/TrainingDay>. The two-day main meeting<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program#Day_1:_July_26.2C_Thursday>includes over 25 talks by Galaxy community members and Galaxy developers addressing the challenges of 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. Galaxy <http://gmod.org/wiki/Galaxy>is an open web-based platform for data intensive biomedical research<http://galaxyproject.org>that is widely used and deployed at research organizations of all sizes around the world. See you in Chicago! Dave Clements, on behalf of the GCC2012 Organizing Committee<http://galaxyproject.org/wiki/Events/GCC2012/Organizing%20Committee> Links: 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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Galaxy Main new native genomes & updated genomes
by Jennifer Jackson 08 Jun '12

08 Jun '12

Dear Galaxy Community, Recent genome additions and updates on the *Galaxy Main public instance* at http://usegalaxy.org include: * New native genome additions:* * *"mm10"*: Mouse (/Mus musculus/) Dec 2011, GRCm38, source UCSC * *"gorGor3"*: Gorilla (/Gorilla gorilla gorilla/) May 2011, WGS CABD02, source UCSC * *"bosTau6"*: Cow (/Bos taurus/) Nov 2009, UMD_3.1, source UCSC * Existing genomes with content updates:* * *"bosTau4, bosTauMd3, canFam2, mm9, panTro3, rn4"* * Details:* * /Native genomes/ are sometimes referred to as "/locally cached/" on tool forms. * New and updated indexes include: /NGS:+/ (all tools), /Lift-Over/ (Convert genome coordinates), and /Fetch Sequences/ (Extract DNA). * Currently, these additions and updates exclude the tools in the group /NGS: GATK Tools (beta)/, however new genomes will be added soon. For now, use the custom reference genome <http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome> option with this tool group, if not using*"Homo sapiens b37 (hg_g1k_v37)"*. * Additional new genomes and updates are in progress and will be announced via Twitter @galaxyproject <http://wiki.g2.bx.psu.edu/Galaxy%20on%20Twitter> and the galaxy-announce(a)bx.psu.edu <http://wiki.g2.bx.psu.edu/Mailing%20Lists#The_lists> mailing list. * Genome requests can be sent to the mailto:galaxy-user@bx.psu.edu <mailto:galaxy-user@bx.psu.edu>mailing list. Please include the full genome name, a link to the stable public source, and any build or species specific information you feel is relevant. This helps us to create a reference genome the entire Galaxy community can use. * Unfinished genomes or genomes not yet published to a stable source repository are still often best used as a custom reference genome <http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome> with tools, but please feel free to check in for feedback. /Thanks for using Galaxy!/ -- Jennifer Jackson http://galaxyproject.org

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GCC2012 Early Registration ends in 1 week
by Dave Clements 04 Jun '12

04 Jun '12

Hello all, Just a reminder that early registration for the 2012 Galaxy Community Conference (GCC2012) <http://galaxyproject.org/wiki/Events/GCC2012>, being held in Chicago, Illinois, July 25-27, *closes on June 11, one week from today*. Registering early saves 36 to 42% on registration costs, and allows you to book discounted conference lodging<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodging> *before it fills up*. Register now<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register> . GCC2012 <http://galaxyproject.org/wiki/Events/GCC2012> is about integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. This 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. Galaxy <http://gmod.org/wiki/Galaxy> is an open web-based platform for data intensive biomedical research <http://galaxyproject.org> that is widely used and deployed at research organizations of all sizes and around the world. The GCC2012 Training Day<http://galaxyproject.org/wiki/Events/GCC2012/TrainingDay>agenda has been finalized. It has 3 parallel tracks, each featuring four, 90 minute workshops and covering 10 different topics. The final schedule<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>of speakers<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program#Confirmed_Speakers>and abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> are also now available. Hope to see you in Chicago! Dave Clements, on behalf of the GCC2012 Organizing Committee<http://galaxyproject.org/wiki/Events/GCC2012/Organizing%20Committee> -- 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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