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 *

And here's how the new papers are categorized:
 * [[http://www.biorxiv.org/content/biorxiv/early/2015/01/10/013615|Merging OpenLifeData with SADI services using Galaxy and Docker]], by Mikel E. Aranguren, ''bioRxiv''
 * [[http://www.biorxiv.org/content/early/2015/01/21/014043|NCBI BLAST+ integrated into Galaxy]], by Peter J. A. Cock, [[JohnChilton|John M. Chilton]], [[BjoernGruening|Björn Grüning]], James E. Johnson, [[NicolaSoranzo|Nicola Soranzo]], ''bioRxiv''
 * [[http://www.gigasciencejournal.com/content/4/1/1/abstract|SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations]], by Wilfried M Guiblet, Kai Zhao, Stephen J O'Brien, Steven E Massey, Alfred L Roca and Taras K Oleksyk, ''[[http://www.gigasciencejournal.com/|GigaScience]]'' 2015, 4:1
   [[http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/g/wguiblet2014|Supplementary materials]] (as a Galaxy Page)

The new papers were related to:
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<<div(right)>>[[http://gcc2015.tsl.ac.uk/|{{attachment:Images/Logos/GCC2015LogoWide600.png|2015 Galaxy Community Conference (GCC2015)|width="100"}}]]<<div>>
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<<div(left)>>[[http://gcc2015.tsl.ac.uk/|{{attachment:Images/Logos/GCC2015LogoWide600.png|Sponsor GCC2015|width="170"}}]]<<div>>

The [[http://gcc2015.tsl.ac.uk/|2015 Galaxy Community Conference (GCC2015)]] is the Galaxy community's annual gathering of users, developers, and administrators. [[Events/GCC2014|Previous GCC's]] have drawn over 200 participants, and we expect that to happen again in 2015. GCC2015 is being hosted by [[http://tsl.ac.uk/|The Sainsbury Lab]] in Norwich, UK, immediately before [[http://www.open-bio.org/wiki/BOSC_2015|BOSC]] and [[http://www.iscb.org/ismbeccb2015|ISMB/ECCB]] in Dublin.

''Early'' registration (save ''heaps)'' and [[http://gcc2015.tsl.ac.uk/abstracts/|abstract submission]] will open later in February. If you work in data-intensive life science research, then it is hard find a meeting more relevant than GCC2015. We look forward to seeing you there.
 

=== Training Day Topic Voting Closes TODAY ===

<<div(right)>>[[http://bit.ly/gcc2015vote|{{attachment:Images/Logos/GCC2015_TrainingDay128.png|Vote now!}}]]
<<div(center)>>
||<class="th"> &nbsp;&nbsp; [[http://bit.ly/gcc2015vote|Vote now!]] &nbsp;&nbsp; ||
<<div>><<div>>

'''[[http://bit.ly/gcc2015vote|Voting]] on what topics should be offered at the [[http://gcc2015.tsl.ac.uk/training-day/|GCC2015 Training Day]] closes today, 30 January.'''

[[http://gcc2015.tsl.ac.uk/training-day/|Topics]] for the [[http://gcc2015.tsl.ac.uk/training-day/|GCC2015 Training Day]] are selected by you, the Galaxy Community. There are [[http://gcc2015.tsl.ac.uk/training-day/|nominated topics]] spanning from basic usage to advanced deployment. No matter what you do with Galaxy, there are topics for you to choose from. Your vote will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters.

The Training Day schedule, including instructors, will be published before early registration opens in February.

'''About the [[http://gcc2015.tsl.ac.uk/training-day/|GCC2015 Training Day]]:'''

The [[http://gcc2015.tsl.ac.uk/|2015 Galaxy Community Conference (GCC2015)]] will start on 6 July with a [[http://gcc2015.tsl.ac.uk/training-day/|Training Day]] featuring parallel tracks, each with several multi-hour workshops. There will be at least one complete track about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances.
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Please let the GCC2015 Organising Committee (<<MailTo(gcc2015-org AT lists DOT galaxyproject DOT org)>>) know if you are interested in helping make this event a success.
Please let the [[http://gcc2015.tsl.ac.uk/|organisers|GCC2015 Organising Committee]] (<<MailTo(gcc2015-org AT lists DOT galaxyproject DOT org)>>) know if you are interested in helping make this event a success.

== 19 February GalaxyAdmins Meetup ==

<<div(right)>>[[Community/GalaxyAdmins/Meetups/2015_02_19|{{attachment:Images/Logos/GalaxyAdmins.png|GalaxyAdmins meetup February 19|width="150"}}]]<<div>>

The first [[Community/GalaxyAdmins|GalaxyAdmins]] [[Community/GalaxyAdmins/Meetups/2015_02_19|meetup of 2015]] will happen online on Thursday, 15 February. [[Community/GalaxyAdmins|GalaxyAdmins]] is a special interest group for Galaxy community members who are responsible for Galaxy installations.

A summary of both the user and admin/developer [[News/2014Questionnaire|2014 Galaxy Community Questionnaires]] will be presented by [[DaveClements|Dave Clements]], a ''Galaxy Project Update'' will be offered by a [[GalaxyTeam|Galaxy Team member]], and [[HansrudolfHotz|Hans-Rudolf Hotz]] will lead a short discussion on ''GalaxyAdmins direction''.

Thanks to everyone for letting us know what dates and times worked best for you. This time and day of the week worked for a remarkable 91% of respondents.
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= GalaxyAdmins is back! =

<<div(right)>>[[Community/GalaxyAdmins|{{attachment:Images/Logos/GalaxyAdmins.png|GalaxyAdmins is back!|width="150"}}]]<<div>>

The first [[Community/GalaxyAdmins|GalaxyAdmins]] meetup of 2015 will happen online on ....

The main presentation for the February meetup will be a summary of the Galaxy Community Survey last fall, presented by [[DaveClements|Dave Clements]]. The survey covered both Galaxy usage and deployment. The survey results will be published online before the call.

''Galaxy-Admins'' is a discussion group for Galaxy community members who are responsible for large Galaxy installations.

In an effort to better serve the global community we will rotate the time of the call in different months to be convenient for different parts of the world. To help us pick the best set of times for the calls, '''please take a few minutes and fill out this [[http://doodle.com/dq3bexyuihs59h3c|Doodle poll]].''' It covers every hour in a 72 hour period. ''Please don't forget to select the timezone before you start filling it out.''
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 * [[News/McMasterOpening|Systems Administrator / Information Technologist]], [[http://mcarthurbioinformatics.ca/|McArthur Lab]] in the [[http://fhs.mcmaster.ca/biochem/|McMaster University Department of Biochemistry & Biomedical Sciences]]  * [[News/MDCBerlinBuchOpening|Bioinformatics scientist/engineer]] for RNA bioinformatics and next-generation sequencing, [[https://www.mdc-berlin.de/|MDC Berlin-Buch]]
 * [[http://bit.ly/1uUGUyh|Bioinformatics Research Officer / Postdoc]], Gene and Stem Cell Therapy, [[http://www.centenary.org.au/|The Centenary Institute]], Sydney, Australia
 * [[http://bit.ly/1JSbytl|Postdoc Position]], Cancer Bioinformatics, [[http://www.vib.be/|VIB]], Leuven, Belgium
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 * [[News/StatisticalGenomicsPostDocPennState|Statistical Genomics Postdoc]] opening in the Makova lab at Penn State
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X new [[PublicGalaxyServers|public Galaxy servers]] were added in January. Several new [[PublicGalaxyServers|public Galaxy servers]] were added in January.
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== CardioVascular Research Grid (CVRG) ==

<<div(right solid)>>[[http://cvrg.galaxycloud.org/|{{attachment:PublicGalaxyServers/CVRGHome.png|CardioVascular Research Grid (CVRG)|}}]]<<div>>

 * ''Links:''
   * [[http://cvrg.galaxycloud.org/|CardioVascular Research Grid (CVRG) Galaxy Server]]
   * [[http://www.cvrgrid.org/|CVRG Project home page]]
 * ''Domain/Purpose:''
   * The !CardioVascular Research Grid (CVRG) project is creating an infrastructure for secure seamless access to study data and analysis tools.
 * ''Comments:''
   * Users can transfer data to CVRG Galaxy at high speed using [[https://www.globus.org/globus-connect-personal|Globus Connect]]. CVRG Galaxy provides a wide range of analysis algorithms, including [[http://www.physionet.org/|Physionet]] algorithms for ECG analysis, and stored workflows that simplify the process of data analysis. CVRG Galaxy also has tools that help users run their analyses faster by using multiple processors on the Amazon Elastic Compute Cloud. CVRG Galaxy can annotate data by retrieving ontology terms from the [[http://bioportal.bioontology.org/|Bioportal]] ontology server.
 * ''User Support:''
   * [[http://wiki.cvrgrid.org/index.php/CVRG_Galaxy|CVRG Galaxy Wiki Page]]
 * ''Quotas:''
   * An account is required; anyone can create an account
 * ''Sponsor(s):''
   * "The CVRG project is supported by the [[http://www.nhlbi.nih.gov/|National Heart Lung & Blood Institute]]. The project is based at the [[http://www.icm.jhu.edu/|Institute for Computational Medicine]] at the Johns Hopkins University, [[https://medschool.vanderbilt.edu/dbmi/|Department of Biomedical Informatics]] at Vanderbilt University Medical Center, [[http://cci.uncc.edu/|The College of Computing and Informatics]] at UNC Charlotte, [[http://cci.emory.edu/cms/index.html|The Center for Comprehensive Informatics]] at Emory University, [[http://www.stonybrook.edu/sb/departments/ceas.shtml|The College of Engineering and Applied Sciences]] at Stony Brook University, and the [[http://www.ci.anl.gov/|Computation Institute]] at The University of Chicago."

== Center for Phage Technology (CPT) ==

<<div(right solid)>>[[https://cpt.tamu.edu/galaxy-public/|{{attachment:PublicGalaxyServers/CPTLogo.png|Center for Phage Technology (CPT)|width="300"}}]]<<div>>

 * ''Links:''
   * [[https://cpt.tamu.edu/galaxy-public/|Center for Phage Technology (CPT) Galaxy Server]]
   * [[https://cpt.tamu.edu/|Center for Phage Technology (CPT) home page]]
   * [[https://cpt.tamu.edu/computer-resources/galaxygetopt/|GalaxyGetOpt]]

 * ''Domain/Purpose:''
   * Phage biology.
 * ''Comments:''
   * Server includes 50 additional tools, and PAUSE (Pile-Up Analysis Using Starts & Ends) V1 and V2 tool sets. There are also several [[https://cpt.tamu.edu/galaxy-public/workflow/list_published|published workflows]] demonstrating PAUSE for both paired and single-end reads.
 * ''User Support:''
   * [[https://cpt.tamu.edu/galaxy-faq-ever-needed-a-question-answered/|FAQ]]
   * Email: <<MailTo(esr+gxfaq@tamu.edu, Eric Rasche)>>
 * ''Quotas:''
   * An account is required; anyone can create an account
 * ''Sponsor(s):''
   * [[https://cpt.tamu.edu/|Center for Phage Technology (CPT)]], Texas A&M University
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== New Galaxy Training Resources == <<div(right)>><<BR>>
[[http://www.irb.hr/eng|{{attachment:Images/Logos/IRBLogo300.jpg|Ruđer Bošković Institute (RBI)|width="135"}}]]<<div>>

== New Galaxy Training Network Member: Ruđer Bošković Institute ==

We are pleased to welcome the [[http://www.irb.hr/|Ruđer Bošković Institute]] in Zagreb, Croatia as the [[Teach/Trainers#Ruđer Bošković Institute (RBI)|newest member]] of [[Teach/GTN|Galaxy Training Network (GTN)]]. Dobrodošli!
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[[News/BioBlendV0.5.2|BioBlend v0.5.2 was released in October]]. [[https://github.com/afgane/bioblend|BioBlend]] is a python library for interacting with CloudMan and the [[Learn/API|Galaxy API]].

New versions of [[GalaxyUpdates/2014_09#August 11, 2014 Galaxy Distribution|Galaxy]], [[GalaxyUpdates/2014_09#August 2014 CloudMan Release|CloudMan]], and [[GalaxyUpdates/2014_09#blend4j 0.1.1 Release|blend4j]] were all released in August.
== Galaxy 2015/01/13 Distribution ==

<<div(right)>>[[http://getgalaxy.org|{{attachment:Images/Logos/GetGalaxyOrg.png|width=175}}]]<<div>>

'''[[http://wiki.galaxyproject.org/DevNewsBriefs/2015_01_13|Complete News Brief]]'''

=== Security ===
Several ''critical'' security vulnerabilities were recently discovered by Bartlomiej Balcerek and colleagues at the Wroclaw Centre for Networking and Supercomputing. This [[DevNewsBriefs/2015_01_13#Security|stable Galaxy release contains fixes for those vulnerabilities]]. '''The Galaxy Team strongly encourages Galaxy server administrators to update their Galaxy servers immediately.'''

=== IPython Integration ===
Thanks to the awesome work of community members Björn Grüning and Eric Rasche, [[DevNewsBriefs/2015_01_13#IPython_Integration|Galaxy now features integration with the popular IPython project]]. The [[https://github.com/bgruening/galaxy-ipython|Galaxy-IPython]] project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker.

=== Tool Form Upgrade (for Beta Testing) ===
In Galaxy's development branch, the basic tool from has been [[DevNewsBriefs/2015_01_13#Tool_Form_Upgrade_.28for_Beta_Testing.29|redesigned and modernized to address certain limitations in Galaxy's responsiveness when working with longer forms containing multiple parameter choices]]. This new tool form will become the default with the next release - but we are hoping tool author's and power users enable it and provide feedback during this release cycle in order to ensure it is working ideally when it becomes the default.

=== Get The Distribution ===
||<|3 style="border: none"> [[http://getgalaxy.org/|{{http://galaxy.psu.edu/static/getgalaxy.png|getgalaxy|width=70}}]] &nbsp;&nbsp; ||<-2 style="border: none"> '''[[http://wiki.galaxyproject.org/Admin/Get%20Galaxy|getgalaxy.org]]''' ||
||<style="border: none"> '''[[http://galaxy-dist.readthedocs.org|galaxy-dist.readthedocs.org]]''' ||<style="border: none"> ||
||<style="border: none"> '''[[http://bitbucket.org/galaxy/galaxy-dist|bitbucket.org/galaxy/galaxy-dist]]''' ||<style="border: none"> ||
||<style="border: none"> ||
||<style="border: none">'''new''': ||<style="border: none"> {{{$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable }}} ||
||<style="border: none"> '''upgrade''': ||<style="border: none"> {{{$ hg pull }}} <<BR>> {{{$ hg update latest_2015.01.13}}} ||


== BioBlend ==
[[News/BioBlendV0.5.2|BioBlend v0.5.2 was released in October]]. [[https://github.com/galaxyproject/bioblend|BioBlend]] is a python library for interacting with CloudMan and the [[Learn/API|Galaxy API]]. In January the [[https://github.com/galaxyproject/bioblend|BioBlend source]] was moved to the [[https://github.com/galaxyproject|galaxyproject Github account]].

== Planemo 0.2.0 ==

Version 0.2.0 of [[https://github.com/galaxyproject/planemo/blob/master/README.rst|Planemo]] was released in January. Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. Updates included:
 * Improvements to way Planemo loads its own copy of Galaxy modules to prevent various conflicts when launching Galaxy from Planemo. ([[https://github.com/galaxyproject/planemo/pull/56|Pull Request 56]])
 * Allow setting various test output options in ``~/.planemo.yml`` and disabling JSON output.
 * More experimental Brew and Tool Shed options that should not be considered part of Planemo's stable API. See [[http://bit.ly/gxbrew1|this presentation]] for more details.
 * Fix ``project_init`` for BSD tar (thanks to [[NiteshTuraga|Nitesh Turaga]] for the bug report.)
 * Documentation fixes for tool linting command (thanks to [[NicolaSoranzo|Nicola Soranzo]]).

== Other ==
New versions [[GalaxyUpdates/2014_09#August 2014 CloudMan Release|CloudMan]], and [[GalaxyUpdates/2014_09#blend4j 0.1.1 Release|blend4j]] were released in August.
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 * An [[http://nbviewer.ipython.org/github/bgruening/notebooks/blob/master/Perl/perl_package_to_galaxy_tool_dependency.ipynb|IPython Notebook that builds Galaxy tool_dependencies.xml file for Perl packages]], from [[BjoernGruening|Bjorn Grüning]]
 * [[http://nsf.gov/awardsearch/showAward?AWD_ID=1443040|NSF Award CIF21 DIBBS: Tripal Gateway, a Platform for Next-Generation Data Analysis and Sharing]] started on January 1. Will integrate [[http://tripal.info/|Tripal]] and Galaxy, and allow Tripal community databases to create and share workflows.
 * [[Dan|Dan Blankenberg]] on a [[https://github.com/galaxyproject/tools-iuc/issues/22#issuecomment-69930103|useful way to handle tools with outputs tied to tool version]] in Galaxy
 * In [[https://bitbucket.org/galaxy/galaxy-central/|galaxy-central]] now: [[https://bitbucket.org/galaxy/galaxy-central/pull-request/634/allow-tools-to-explicitly-produce-dataset/diff|tools can explicitly produce collections of datasets]]
 * [[http://genomeintelligence.org/?p=745|Getting your 23 and Me data into Galaxy]], at [[http://genomeintelligence.org/|Genome Intelligence]]

== And a Huge Thank You! ==

The [[GalaxyTeam|Galaxy Team]] would like to thank everyone who took the time to respond to the project's [[News/GalaxyProjectGrantSupport|call for support]]. The project's main grant was submitted in January. This is yet another example of how Galaxy greatly benefits from the community.

Hey! This is under construction!

February 2015 Galaxy Update

Galaxy Updates

Welcome to the February Galaxy Update, a summary of what is going on in the Galaxy community. Galaxy Updates complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

New Papers

xx papers referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in January. Some highlights:

The new papers were related to:

#

Tag

  

#

Tag

  

#

Tag

  

#

Tag

-

Cloud

-

Project

-

Tools

-

UsePublic

-

HowTo

-

RefPublic

-

UseCloud

-

Visualization

-

IsGalaxy

-

Reproducibility

-

UseLocal

-

Workbench

-

Methods

-

Shared

-

UseMain

Events

GCC2015: 6-8 July, Norwich UK

Sponsor GCC2015

The 2015 Galaxy Community Conference (GCC2015) is the Galaxy community's annual gathering of users, developers, and administrators. Previous GCC's have drawn over 200 participants, and we expect that to happen again in 2015. GCC2015 is being hosted by The Sainsbury Lab in Norwich, UK, immediately before BOSC and ISMB/ECCB in Dublin.

Early registration (save heaps) and abstract submission will open later in February. If you work in data-intensive life science research, then it is hard find a meeting more relevant than GCC2015. We look forward to seeing you there.

Training Day Topic Voting Closes TODAY

Vote now!

   Vote now!   

Voting on what topics should be offered at the GCC2015 Training Day closes today, 30 January.

Topics for the GCC2015 Training Day are selected by you, the Galaxy Community. There are nominated topics spanning from basic usage to advanced deployment. No matter what you do with Galaxy, there are topics for you to choose from. Your vote will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters.

The Training Day schedule, including instructors, will be published before early registration opens in February.

About the GCC2015 Training Day:

The 2015 Galaxy Community Conference (GCC2015) will start on 6 July with a Training Day featuring parallel tracks, each with several multi-hour workshops. There will be at least one complete track about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances.

GenomeWeb Sponsors GCC2015

We are happy to announce that GenomeWeb is a Silver Sponsor for GCC2015.

GenomeWeb
  • GenomeWeb is an independent online news organization based in New York. Since 1997, GenomeWeb has served the global community of scientists, technology professionals, and executives who use and develop the latest advanced tools in molecular biology research and molecular diagnostics. Our editorial mission is to cover the scientific and economic ecosystem spurred by the advent of high-throughput genome sequencing. We operate the largest online newsroom focused on advanced molecular research tools in order to provide our readers with exclusive news and in-depth analysis of this rapidly evolving market.

Call for Sponsors

The 2015 Galaxy Community Conference (GCC2015) is now accepting Sponsorships. Your organisation can play a prominent part in the Galaxy community by sponsoring GCC2015. Sponsorship is an excellent way to raise your organization’s visibility.

Several sponsorship levels are available, including two levels of premier sponsorships that include presentations. Premium sponsorships are limited, however, so you are encouraged to act soon.

Please let the organisers (<gcc2015-org AT lists DOT galaxyproject DOT org>) know if you are interested in helping make this event a success.

19 February GalaxyAdmins Meetup

GalaxyAdmins meetup February 19

The first GalaxyAdmins meetup of 2015 will happen online on Thursday, 15 February. GalaxyAdmins is a special interest group for Galaxy community members who are responsible for Galaxy installations.

A summary of both the user and admin/developer 2014 Galaxy Community Questionnaires will be presented by Dave Clements, a Galaxy Project Update will be offered by a Galaxy Team member, and Hans-Rudolf Hotz will lead a short discussion on GalaxyAdmins direction.

Thanks to everyone for letting us know what dates and times worked best for you. This time and day of the week worked for a remarkable 91% of respondents.

Other Events

http://bit.ly/gxycal

There are upcoming events on XXXXXXXXXX. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Date

Topic/Event

Venue/Location

Contact

Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the Galaxy News feed and include it in next month's update.


New Public Servers

Several new public Galaxy servers were added in January.

RiboGalaxy

RiboGalaxy
  • Link:

  • Domain/Purpose:

    • RiboGalaxy provides on-line tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique.

  • Comments:

    • RiboGalaxy is a freely available web server for processing and analysing ribosome profiling (ribo-seq) data with the visualization functionality provided by GWIPS-viz. RiboGalaxy provides a compact suite of tools specifically tailored for the alignment and visualization of ribo-seq and corresponding mRNA-seq data. Users can take advantage of the published workflows on RiboGalaxy which reduce the multi-step alignment process to a minimum of inputs.

  • User Support:

  • Quotas:

    • Anonymous users can use RiboGalaxy. However, the upload and processing of datasets larger than 2GB and the use of advanced features such as published workflows, will require the user to be registered on RiboGalaxy.

  • Sponsor(s):

CardioVascular Research Grid (CVRG)

CardioVascular Research Grid (CVRG)

Center for Phage Technology (CPT)

Center for Phage Technology (CPT)

Galaxy Community Hubs


Ruđer Bošković Institute (RBI)

New Galaxy Training Network Member: Ruđer Bošković Institute

We are pleased to welcome the Ruđer Bošković Institute in Zagreb, Croatia as the newest member of Galaxy Training Network (GTN). Dobrodošli!

Several new Training Resources were added in January:

New Releases

Galaxy 2015/01/13 Distribution

width=175

Complete News Brief

Security

Several critical security vulnerabilities were recently discovered by Bartlomiej Balcerek and colleagues at the Wroclaw Centre for Networking and Supercomputing. This stable Galaxy release contains fixes for those vulnerabilities. The Galaxy Team strongly encourages Galaxy server administrators to update their Galaxy servers immediately.

IPython Integration

Thanks to the awesome work of community members Björn Grüning and Eric Rasche, Galaxy now features integration with the popular IPython project. The Galaxy-IPython project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker.

Tool Form Upgrade (for Beta Testing)

In Galaxy's development branch, the basic tool from has been redesigned and modernized to address certain limitations in Galaxy's responsiveness when working with longer forms containing multiple parameter choices. This new tool form will become the default with the next release - but we are hoping tool author's and power users enable it and provide feedback during this release cycle in order to ensure it is working ideally when it becomes the default.

Get The Distribution

getgalaxy   

getgalaxy.org

galaxy-dist.readthedocs.org

bitbucket.org/galaxy/galaxy-dist

new:

$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable 

upgrade:

$ hg pull 
$ hg update latest_2015.01.13

BioBlend

BioBlend v0.5.2 was released in October. BioBlend is a python library for interacting with CloudMan and the Galaxy API. In January the BioBlend source was moved to the galaxyproject Github account.

Planemo 0.2.0

Version 0.2.0 of Planemo was released in January. Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. Updates included:

  • Improvements to way Planemo loads its own copy of Galaxy modules to prevent various conflicts when launching Galaxy from Planemo. (Pull Request 56)

  • Allow setting various test output options in ~/.planemo.yml and disabling JSON output.

  • More experimental Brew and Tool Shed options that should not be considered part of Planemo's stable API. See this presentation for more details.

  • Fix project_init for BSD tar (thanks to Nitesh Turaga for the bug report.)

  • Documentation fixes for tool linting command (thanks to Nicola Soranzo).

Other

New versions CloudMan, and blend4j were released in August.


Galaxy ToolShed

ToolShed Contributions

Galaxy Project ToolShed Repos

Here are new contributions for the past month.

In no particular order:

Tools

Tool Suites

Packages / Tool Dependency Definitions

Select Updates

Other News

And a Huge Thank You!

The Galaxy Team would like to thank everyone who took the time to respond to the project's call for support. The project's main grant was submitted in January. This is yet another example of how Galaxy greatly benefits from the community.