Question: Galaxy November 14, 2012 Distribution & News Brief
0
gravatar for Jennifer Hillman Jackson
5.5 years ago by
United States
Jennifer Hillman Jackson24k 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/
gff cufflinks rna-seq • 662 views
ADD COMMENTlink written 5.5 years ago by Jennifer Hillman Jackson24k
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