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December 2012 Galaxy Update
by Dave Clements 30 Nov '12

30 Nov '12

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Galaxy November 14, 2012 Distribution & News Brief
by Jennifer Jackson 14 Nov '12

14 Nov '12

*Galaxy November 14, 2012 Distribution & News Brief <http://wiki.galaxyproject.org/News/2012_11_14_DistributionNewsBrief>* * Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14> * *Highlights:* * *NGS: Picard (beta)* have moved from the *Galaxy distribution <https://bitbucket.org/galaxy/galaxy-dist>* to the*Galaxy Main Tool Shed* <http://toolshed.g2.bx.psu.edu/>. * The *Galaxy Project* is now using /Sphinx <http://sphinx-doc.org/> Python/ to document the *galaxy-central <http://galaxy-central.readthedocs.org>* and *galaxy-dist* <http://galaxy-dist.readthedocs.org> code base. * The *Intergalactic Utilities Commission* <http://wiki.g2.bx.psu.edu/ReviewingToolShedRepositories> will soon begin reviewing repositories in the *Galaxy Main Tool Shed <http://toolshed.g2.bx.psu.edu/>* (better repos, better tools) * *Tool Shed <http://toolshed.g2.bx.psu.edu/>* *"best practice"* advice: a single tool or a suite of tools per repository? <http://wiki.galaxyproject.org/AToolOrASuitePerRepository> * *Tophat <http://tophat.cbcb.umd.edu/>*, *Tophat2 <http://tophat.cbcb.umd.edu/manual.html>*, and *Cuffdiff <http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff>* *updated* to accept gene annotations in *GFF3 <http://wiki.galaxyproject.org/Learn/Datatypes#GFF3>* format. * Multiple *enhancements* to the *API* <http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14#API>targeting user and history actions. * Plus *updates to* *CloudLaunch <http://usegalaxy.org/cloud>*, new *Security Fixes* <http://wiki.galaxyproject.org/DevNewsBriefs/2012_11_14#Security_Fixes>, and several usability enhancements for *Datasets*, *Datatypes*, *Tools*, and *Tool Shed* functions. / http://getgalaxy.org/////// /http://bitbucket.org/galaxy/galaxy-dist/ /http://galaxy-dist.readthedocs.org/ new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r 5dcbbdfe1087 *Thanks for using Galaxy!* Jennifer Jackson <http://wiki.galaxyproject.org/JenniferJackson> & the Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team> /http://galaxyproject.org/

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GalaxyAdmins meeting -- Nov 14 at 10 AM Central
by IIHG Galaxy Administrator 13 Nov '12

13 Nov '12

Hello, The next meeting of the GalaxyAdmins group will be held on November 14 at 10 AM Central time. Curtis Hendrickson of the University of Alabama Birmingham's Center for Clinical and Translational Science (UAB CCTS) will speak on "Deploying Galaxy on a shared-node cluster at UAB". The meeting will also include time for open discussion. Your active participation is encouraged. Thank you! Notes: * Link to the webinar: https://globalcampus.uiowa.edu:443/join_meeting.html?meetingId=1262339408056<https://globalcampus.uiowa.edu/join_meeting.html?meetingId=1262339408056> * Meeting invite is attached * This information is also posted at http://wiki.galaxyproject.org/News/2012_11GalaxyAdmins -- Srinivas Maddhi Senior Systems Administrator Iowa Institute for Human Genetics The University of Iowa

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November 2012 Galaxy Update
by Dave Clements 31 Oct '12

31 Oct '12

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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>

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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

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October 2012 Galaxy Update
by Dave Clements 01 Oct '12

01 Oct '12

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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

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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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