*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.orghttp://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.orghttp://usegalaxy.org
Bonjour à tous,
Avec l'aide et le soutien de l'équipe Galaxy, nous venons de mettre en
ligne la liste de diffusion Galaxy France.
Cette liste a pour but de partager et communiquer sur nos différentes
expériences avec Galaxy au sein de l'hexagone.
La langue officielle de cette liste est le français.
Vous avez besoin d'aide dans l'utilisation de Galaxy,
Vous hébergez un serveur public Galaxy,
Vous maintenez une instance locale de Galaxy,
Vous venez de déposer un outil sur le toolshed,
Vous avez des trucs et astuces pouvant interresser la communauté,
Vous organisez des formations avec Galaxy,
Rejoignez nous en vous inscrivant à
http://lists.bx.psu.edu/listinfo/galaxy-france
Les archives de cette liste sont disponibles à
http://france.list.galaxyproject.org
A très bientôt sur la liste Galaxy France,
Les administrateurs:
Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer
Jackson
------------------------------
---------------------
Hi everyone,
With the help and the support of the Galaxy team, we just put online the
Galaxy French mailing list.
The aim of this list is to share and communicate on our different
experiences with Galaxy in France.
* The main language is French.
*
Topics include, but are not limited to:
You need help in the use of Galaxy,
You're hosting a Galaxy public server,
You're maintaining a local instance of Galaxy,
You just add a new tool on the toolshed,
You have some tips that could interested the community,
You organize workshops with Galaxy,
Join us by subscribing at http://lists.bx.psu.edu/listinfo/galaxy-france
The list's archives are also available at
http://france.list.galaxyproject.org
See you soon on the Galaxy-France list,
The administrators:
Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer
Jackson
--
<http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/http://getgalaxy.org/http://usegalaxy.org/http://galaxyproject.org/wiki/
Galaxy July 20, 2012 Distribution & News Brief
*Complete News Brief
http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_07_20*
*Highlights:
http://wiki.g2.bx.psu.edu/News/Jul202012%20Distribution%20News%20Brief*
*
*Freebayes *has moved from the /Galaxy distribution to the Galaxy's
Main Tool Shed/
*
*EMBOSS* version 5.0.0 tool dependencies in the emboss_5 repository
of the Galaxy Main Tool Shed updated to include information for
automatically installing.
*
*Tool Shed* now also supports specifying the third party tool
dependencies to be automatically installed in new repositories
*
*Admin Genome Indexing* is now in /BETA/. Download, index, and track
progress right from the admin UI!
*
*Improved Error Handling* that captures EXIT codes, STDOUT, and
STDERR from tools in XML. Be sure to read full details.
*
*TopHat2/Bowtie2* latest support includes option to 'report
discordant pairs', updated tests, and more preset options.
*
*Trackster* new parameter space visualization. /Includes BRAND NEW
Features!!/ More details coming soon, but give a test drive now.
*http://getgalaxy.org*
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r ec29ce8e27a1
*Thanks for using Galaxy!*
We hope to see everyone in /Chicago/ @ *GCC2012*!!
The Galaxy Team
Dear Galaxy Community,
Recent genome additions and updates on the *Galaxy Main public instance*
at http://usegalaxy.org include:
*
New native genome additions:*
* *"mm10"*: Mouse (/Mus musculus/) Dec 2011, GRCm38, source UCSC
* *"gorGor3"*: Gorilla (/Gorilla gorilla gorilla/) May 2011, WGS
CABD02, source UCSC
* *"bosTau6"*: Cow (/Bos taurus/) Nov 2009, UMD_3.1, source UCSC
*
Existing genomes with content updates:*
* *"bosTau4, bosTauMd3, canFam2, mm9, panTro3, rn4"*
*
Details:*
* /Native genomes/ are sometimes referred to as "/locally cached/" on
tool forms.
* New and updated indexes include: /NGS:+/ (all tools), /Lift-Over/
(Convert genome coordinates), and /Fetch Sequences/ (Extract DNA).
* Currently, these additions and updates exclude the tools in the
group /NGS: GATK Tools (beta)/, however new genomes will be added
soon. For now, use the custom reference genome
<http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome> option
with this tool group, if not using*"Homo sapiens b37 (hg_g1k_v37)"*.
* Additional new genomes and updates are in progress and will be
announced via Twitter @galaxyproject
<http://wiki.g2.bx.psu.edu/Galaxy%20on%20Twitter> and the
galaxy-announce(a)bx.psu.edu
<http://wiki.g2.bx.psu.edu/Mailing%20Lists#The_lists> mailing list.
* Genome requests can be sent to the mailto:galaxy-user@bx.psu.edu
<mailto:galaxy-user@bx.psu.edu>mailing list. Please include the full
genome name, a link to the stable public source, and any build or
species specific information you feel is relevant. This helps us to
create a reference genome the entire Galaxy community can use.
* Unfinished genomes or genomes not yet published to a stable source
repository are still often best used as a custom reference genome
<http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome> with
tools, but please feel free to check in for feedback.
/Thanks for using Galaxy!/
--
Jennifer Jackson
http://galaxyproject.org