Nominate topics for the 2013 Galaxy Community Conference (GCC2013) Training Day
by Dave Clements
Hello all,
Nominations are now open <http://bit.ly/gcc2013nom> for Training Day
topics<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay>at the
2013
Galaxy Community Conference
(GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013>.
GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30
June with a Training Day featuring 4 parallel tracks, each with three, two
hour workshops, for a total of twelve sessions.
Any topic of interest to the Galaxy Community can be
nominated<http://bit.ly/gcc2013nom>(see what
was offered at GCC2012<http://wiki.galaxyproject.org/Events/GCC2012/TrainingDay>).
Topics can be repeats from last year or brand new, and you are encouraged
to nominate as many topics as you like. The 2013 Galaxy Community
Conference (GCC2013) <http://wiki.galaxyproject.org/Events/GCC2013> will
start on 30 June with a Training Day featuring 4 parallel tracks, each with
three, two hour workshops, for a total of twelve sessions. Nominations will
be compiled into a uniform list, and then topics will be voted on by the
Galaxy Community starting in late January.
Topic nomination closes 11 January.
Thanks,
Dave Clements, on behalf of the GCC2013 Organizing
Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers#Organizing_Committee>
Links:
http://bit.ly/gcc2013nom - nominate a topic
http://bit.ly/gcc2013td - Training Day page
http://galaxyproject.org/GCC2013 - Conference home page
http://bit.ly/gcc2013prom - help get the word out
--
<http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/
9 years, 9 months
Galaxy December 20, 2012 Distribution & News Brief
by Jennifer Jackson
*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-datat...>*,
*#85
<https://bitbucket.org/galaxy/galaxy-central/pull-request/85/another-round...>*,
*#90
<https://bitbucket.org/galaxy/galaxy-central/pull-request/90/patch-to-make...>*,
*#91*
<https://bitbucket.org/galaxy/galaxy-central/pull-request/91/fixing-missin...>.
*
*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
9 years, 9 months
December 3, 2012 Distribution & News Brief
by Jennifer Jackson
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_frame...>,
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
9 years, 10 months