Question: Galaxy November 14, 2012 Distribution & News Brief
0
Jennifer Hillman Jackson ♦ 25k wrote:
*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_f="" ixes="">,
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/