- galaxy-announce - lists.galaxyproject.org

Galaxy October 23, 2012 Distribution & News Brief
by Jennifer Jackson 24 Oct '12

24 Oct '12

*Galaxy Oct 23, 2012 Distribution & News Brief */http://wiki.g2.bx.psu.edu/2012_10_23_DistributionNewsBrief/* * * * *Highlights: * /http://wiki.g2.bx.psu.edu/News/ * *Important Security Fix <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix>* - upgrade *NOW*. * *New Trello Issue Board <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#New_Trello_Issue_Board>* - Learn how to submit, vote, and comment on tickets. * *http://wiki.g2.bx.psu.edu/Tool Shed <http://wiki.g2.bx.psu.edu/Tool%20Shed>* direct updates and changes in Galaxy <http://usegalaxy.org> improve metadata updating, repository management, and more control over tool config. * Updates to the *Visualization <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#Visualization_framework>* tool set cover *Trackster*, *Circster*, and new *Scatter Plot* tool. That's an example plot below. scatterplot-partialscreen <http://usegalaxy.org> * New *API <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#API>* fixes, tuneups, and brand-new methods to control libraries. * Multiple *Admin <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#Source>* changes enable better access to user data to solve problems. *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 12fcd068b12e *Thanks for using Galaxy!* Jennifer Jackson <http://wiki.g2.bx.psu.edu/JenniferJackson> & the Galaxy Team <http://wiki.g2.bx.psu.edu/Galaxy%20Team>

1 0

Galaxy October 5, 2012 Distribution & News Brief
by Jennifer Jackson 05 Oct '12

05 Oct '12

*Galaxy October 5, 2012 Distribution & News Brief* /http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05/ /* Highlights:* http://wiki.g2.bx.psu.edu/News / ** * *BWA <http://bio-bwa.sourceforge.net/>* tool wrappers /migrated <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#BWA_Migration_to_Tool_Sh…>/ to the *Galaxy Main Tool Shed <http://toolshed.g2.bx.psu.edu/>*. * *Tool Factory* paper has been /E Published <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Galaxy_Tool_Factory_Pape…>/ in PubMed <http://www.ncbi.nlm.nih.gov/pubmed> at *PMID: 23024011 <http://www.ncbi.nlm.nih.gov/pubmed/23024011>*. * The *Tool Shed Wiki <http://wiki.g2.bx.psu.edu/Tool%20Shed>* wiki has been re-written with a new, cleaner presentation. And check out all the /new features <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Tool_Shed>/! * Accessible *tool versions* in the UI and *new exit code features* enable /clearer experimental tracking and ease reproducibility <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Tools>/. * Release also includes *Visualization <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Visualization_framework>* updates, a new admin tool for /PostgreSQL <http://www.postgresql.org>/ *Dataset cleanup <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Dataset_Cleanup>*, and improvements in *API <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#AP>* , *Workflow <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Workflows>*, and *Security <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_05#Security_Fixes>* components. 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 b5bda7a5c345 ** * Thanks for using Galaxy!* Jennifer Jackson & Galaxy Team http://galaxyproject.org

1 0

October 2012 Galaxy Update
by Dave Clements 01 Oct '12

01 Oct '12

1 0

Galaxy September 20, 2012 Distribution & News Brief
by Jennifer Jackson 21 Sep '12

21 Sep '12

*Galaxy September 20, 2012 Distribution & News Brief* http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_20 <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_20> /*Highlights:* http://wiki.g2.bx.psu.edu/News <http://wiki.g2.bx.psu.edu/News>/ * A /*new Galaxy tool*/<http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_20#Galaxy_Tool_Factory> that writes other /*new Galaxy tools*/! The /*Tool Factory*/ is in the Galaxy's Main *Tool Shed* (*/toolfactory/*). Try it now! * Learn how to *display multiple versions of a tool* in the Galaxy tool panel. * *CloudLaunch Overhaul* includes Boto 2.5.2 and simplified instance selection and key generation. * Release also includes more *Tool Shed *updates, *Framework* and *API* updates, plus *Security* and *Bug* fixes. http://getgalaxy.org http://bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist> *new: * $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist* upgrade:* $ hg pull -u -r da9d740fce31 ** *Thanks for using Galaxy!* Jennifer Jackson & Galaxy Team http://galaxyproject.org

1 0

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

1 0

September 2012 Galaxy Update
by Dave Clements 29 Aug '12

29 Aug '12

1 0

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/

1 0

August 2012 Galaxy Update
by Dave Clements 31 Jul '12

31 Jul '12

1 0

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

1 0

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/

1 0