- galaxy-announce - lists.galaxyproject.org

January 2013 Galaxy Update
by Dave Clements 02 Jan '13

02 Jan '13

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Galaxy December 20, 2012 Distribution & News Brief
by Jennifer Jackson 20 Dec '12

20 Dec '12

*Galaxy Dec 20, 2012 Distribution & News Brief <http://wiki.galaxyproject.org/News/2012_12_20_DistributionNewsBrief>* *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_20>* *Highlights:* * *Required Metadata Reset* for instances running *Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed>* repositories. Be sure to *learn how <http://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories>*. * *Simplified tool config*: all tools (including tool shed repos) can now have handlers and runners assigned based on their "short id". * *New* GFF <http://wiki.galaxyproject.org/Learn/Datatypes#GFF>/GFF3 <http://wiki.galaxyproject.org/Learn/Datatypes#GFF3> annotation support for *Cuffcompare/merge/diff <http://cufflinks.cbcb.umd.edu/manual.html>*. * *More Updated* tools: *TopHat2 <http://tophat.cbcb.umd.edu/manual.html>*, *Bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml>*. * *Multiple pull-requests* contributed by community (thanks!): *#83 <https://bitbucket.org/galaxy/galaxy-central/pull-request/83/allow-a-datatyp…>*, *#85 <https://bitbucket.org/galaxy/galaxy-central/pull-request/85/another-round-o…>*, *#90 <https://bitbucket.org/galaxy/galaxy-central/pull-request/90/patch-to-make-e…>*, *#91* <https://bitbucket.org/galaxy/galaxy-central/pull-request/91/fixing-missing-…>. * *Issue tracking help* is now covered in detailed in our new wiki: *Using the Galaxy Issue Board <http://wiki.galaxyproject.org/Issues>* * *GCC2013 Training Day Topic Nominations <http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> are now open* through /*January 11th*/ <http://wiki.galaxyproject.org/Events/GCC2013/KeyDates> * *Plus* more *Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed>* updates, *Bug Fixes*, and improvements to *Trackster, UI, Libraries, and Histories*. * getgalaxy.org <http://getgalaxy.org>* *bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* *galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org> * new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r 36ad8aa7b922 *Best wishes for a safe and happy holiday*, /*The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>*/ -- Jennifer Jackson http://galaxyproject.org

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December 3, 2012 Distribution & News Brief
by Jennifer Jackson 03 Dec '12

03 Dec '12

December 3, 2012 Distribution & News Brief <http://wiki.galaxyproject.org/News/2012_12_03_DistributionNewsBrief> * Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2012_12_03>* * Highlights:* * *NGS: Mapping* tools *Bowtie <http://bowtie-bio.sourceforge.net/index.shtml>* and *Lastz <http://www.bx.psu.edu/%7Ersharris/lastz/>* have moved from the *Galaxy distribution <https://bitbucket.org/galaxy/galaxy-dist>* to the *Galaxy Main Tool Shed <http://toolshed.g2.bx.psu.edu/>*. * Improvements in the display of *Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed>* repository dependencies and contents. * More *Tool Shed <http://toolshed.g2.bx.psu.edu/>* updates including details of the Functional test framework <http://wiki.galaxyproject.org/HostingALocalToolShed#Functional_test_framewo…>, a new hgweb.config file and HgWebConfigManager tool, plus other management features. * Updated *UI* display and functionality for datasets and histories: new *paused* state and "resume/paused" toggle, new *History menu options*, and improved *Scatterplot* visualizations. * The *SGE* job runner has now been fully deprecated and replaced with *DRMAA*. * Several enhancements to aid with *reproducibility*: "Re-run" and "Extract workflow" validates datasets and tools, respectively, and a new data tables registry within the Administration menu, along with associated tools, corrects or warns about tool migration issues. * Highlights from the new Galaxy *CloudMan <http://usegalaxy.org/cloud>* release and /*December 2012 Galaxy Update <http://wiki.galaxyproject.org/GalaxyUpdates/2012_12>*/. * 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 f364d992270c * Thanks for using Galaxy!* The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team> -- Jennifer Jackson http://galaxyproject.org

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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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