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Wiki Migration is Underway

written 9 months ago by Galaxy News

The wiki migration is part of a general overhaul of Galaxy documentation that started with the creation of docs.galaxyproject.org. We also plan to move most admin documentation inside of Galaxy releases, and to support community maintainable training materials. We are migrating the Galaxy wiki from MoinMoin to a GitHub based solution using GitHub Flavored Markdown for content, and the Metalsmith static site generator to render the actual site. The move to GitHub will allow us to take full advantage of GitHub's collaboration features and will move the documentation to a source format (Markdown) that more people are familiar with. Using Metalsmith to generate the site will give us much more flexibility in how we present semi-structured content such as the events calendar, the public Galaxy servers list, and the GTN trainer and training resources directories. You'll be able to update the documentation entirely on GitHub. If you are inclined to go deeper you can clone the repository, make changes, and build and serve the entire site locally. The migration has started. This wiki has been frozen. We will bring up a beta version of the new site at a different URL within a few days. We then expect a flurry of activity while the team and the community make improvements to the new site before it goes official. We'll include guides on how to use the new setup, and what you'll need to know if you decide to dive into Metalsmith. Posted to the Galaxy News on 2016-11-10-- Delivered by ...

Wiki Migration is Underway

written 11 months ago by Galaxy News

The wiki migration is part of a general overhaul of Galaxy documentation that started with the creation of docs.galaxyproject.org. We also plan to move most admin documentation inside of Galaxy releases, and to support community maintainable training materials. We are migrating the Galaxy wiki from MoinMoin to a GitHub based solution using GitHub Flavored Markdown for content, and the Metalsmith static site generator to render the actual site. The move to GitHub will allow us to take full advantage of GitHub's collaboration features and will move the documentation to a source format (Markdown) that more people are familiar with. Using Metalsmith to generate the site will give us much more flexibility in how we present semi-structured content such as the events calendar, the public Galaxy servers list, and the GTN trainer and training resources directories. You'll be able to update the documentation entirely on GitHub. If you are inclined to go deeper you can clone the repository, make changes, and build and serve the entire site locally. The migration has started. This wiki has been frozen. We will bring up a beta version of the new site at a different URL within a few days. We then expect a flurry of activity while the team and the community make improvements to the new site before it goes official on November 21. We'll include guides on how to use the new setup, and what you'll need to know if you decide to dive into Metalsmith. Posted to the Galaxy News on ...

November 2016 Galactic News

written 11 months ago by Galaxy News

The November Galactic News is out and upcoming events are again prominent: Galaxy Australasia Meeting (GAMe 2017): February 3-9, Melbourne, Victoria, Australia. Talk abstracts are due 30 November Bioconda Contribution Fest: November 2-3, Online European Galaxy Developer Workshop, 16-19 January, Strasbourg, France Registration is open and space is limited. Galaxy Admin Training: November 7-11, Salt Lake City, Utah. Reports form the Galaxy Training Material Contribution Fest and Swiss-German Galaxy Days And of course, other upcoming events too There is also the new Arabic speaking Galaxy Community, 87 new publications (including six featured pubs), seven open positions, four new public Galaxy servers and a Jetstream update, one new GTN member and four new training resources, new releases of galaxy-lib &amp; Planemo, and new TooShed contributions. We hope to see you in Melbourne, Strasbourg, Salt Lake, online, and around the world, Dave Clements and the Galaxy Team Posted to the Galaxy News on 2016-10-31-- Delivered by Feed43 service

Galaxy Arabic Community

written 11 months ago by Galaxy News

أرشيف للقائمة البريدية جالاكسي بالعربية يحتوي على الاخبار والمناقشات والاعلانات الخاصة بمستخدمي جالاكسي من البلاد الناطقة بالعربية نرحب بانضمام أي شخص مهتم بالجلاكسي بلاتفورم جالاكسي هي بلاتفورم لتحليل المعلومات الحيوية باستخدام أدوات برمجة أونلاين مجانا تتميز بأنها متاحة للجميع ونتائجها تتميز بالشفافية وبالقدرة على الحصول على نفس النتائج عند إجراء التحليل مرات عديدة. السهولة : يمكن لأي شخص استخدام جالاكسي حتى لو لم تكن لديه خبرة كافية بتحليل المعلومات الحيوية النتائج : تحصل على نفس النتائج مهما أجريت التجربة مرات عديدة وهذا يميز جالاكسي عن العديد من الأدوات الاخرى الشفافية : يمكنك أن تشارك ما توصلت إليه مع زملائك والعالم كله ويمكنك النشر أيضا . جالاكسي مفتوحة لكل المنظمات والسرفر الرئيسي يمكنك من إجراء تحليل على المعلومات الجينية وإيضا توجد مواد تعليمية للتدريب وأماكن العمل وخدمات النشر يمكنك استخدام جالاكسي أونلاين ويمكنك أيضا تنزيلها على الكمبيوتر الخاص بك واستخدامها We are pleased to announce the launch of the Galaxy Arabic community. Galaxy Arabic supports and promotes Galaxy activity for the Arabic speaking community and in Arabic speaking regions of the world. If you are interested in joining the community, please Follow @Galaxy_Arabic on Twitter Join the Galaxy Arabic mailing list. Regional Galaxy news will be posted here, and you can also ask fellow Arabic speakers support questions. Join the Galaxy Arabic Facebook group We look forward to connecting and growing the Arabic speaking Galaxy community. Thanks, Abdelazeem Abdelhameed &lt;abdelazeem_abdelhameed2015505@yahoo.com&gt; and Dave Clements Posted to the Galaxy News on 2016-10-27-- Delivered by Feed43 service

Galaxy on Jetstream Cloud update

written 11 months ago by Galaxy News

Galaxy release 16.07 is now available for free on the Jetstream cloud. This image contains the updated Galaxy application with a toolset that closely matches that of the public Galaxy server available at usegalaxy.org as well as a complete set of reference genomes available on that same server. Availability of the reference data was realized by enabling a connection to a (CVMFS-based) replica server that offers access to approximately 3TB of reference data (vs. ~50GB in the previous version of the image). An additional benefit of such integration is that the reference data is no longer stored on the machine image, reducing the size of that image to about 10GB, leaving more space for the analysis data. The base operating system is Ubuntu 14.04. The image was built using the cloud_setup flavor of the GalaxyKickStart Ansible playbook. Posted to the Galaxy News on 2016-10-17-- Delivered by Feed43 service

Galaxy on Jetstream Cloud update

written 12 months ago by Galaxy News

Galaxy release 16.07 is now available for free on the Jetstream cloud. This image contains the updated Galaxy application with a toolset that closely matches that of the public Galaxy server available at usegalaxy.org as well as a complete set of reference genomes available on that same server. Availability of the reference data was realized by enabling a connection to a (CVMFS-based) replica server that offers access to approximately 3TB of reference data (vs. ~50GB in the previous version of the image). An additional benefit of such integration is that the reference data is no longer stored on the machine image, reducing the size of that image to about 10GB, leaving more space for the analysis data. The base operating system is Ubuntu 14.04. The image was built using the cloud_setup flavor of the GalaxyKickStart Ansible playbook. October 2016 Galactic News The October Galaxy News is hot off the presses and upcoming events are prominent: Galaxy training contribution fest: October 6-7, Online Swiss-German Galaxy Days: October 20-21, Freiburg, Germany Galaxy &amp; Hacktoberfest: Month of October, online Bioconda Contribution Fest: November 2-3, Online Galaxy Admin Training: November 7-11, Salt Lake City, Utah. On time registration ends October 16 Galaxy Australasia Meeting (GAMe 2017): February 3-9, Melbourne, Victoria, Australia. Registration and abstract submission are now open. And of course, other upcoming events too There are also 117 new publications (including six featured pubs), four open positions, two new public Galaxy servers and one new semi-public Galaxy service, new releases of galaxy-lib &amp; ...

Galaxy Admin Training, Nov 7-11

written 12 months ago by Galaxy News

November 7-11, 2016 University of Utah Salt Lake City, Utah United States Registration is open We are pleased to announce that registration for Galaxy Admin Training 2016 is now open. Galaxy Admin Training 2016 is a weeklong event offering basic and advanced sessions. It is being held in Salt Lake City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16) meets in Salt Lake. Basics Session: November 7-8 This two day basics session will introduce participants to what you need to know to get a Galaxy server up and running on a standalone server. You'll also learn how to extend your Galaxy with your own tools and tools from the community, and how to define reference data in your server as well. Advanced Session: November 9-11 The three day advanced session will build on topics covered in the basics section. This session both extends those topics, such as tool definition, and adds new ones, such as working with compute clusters and heterogeneous resources. The goal of the advanced workshop is to enable Galaxy administrators to create robust, high-performance Galaxy instances that take full advantage of available tools and compute and storage resources. Register by September 19 and save up to $130 off standard registration rates (and up to $250 if you work in industry). Galaxy Admin Training 2016 is hosted by the University of Utah Center for High Performance Computing (CHPC), the Department of Biomedical Informatics and the Clinical &amp; Translational Science Biomedical Informatics Core (CCTS BMIC) at the ...

Galaxy Australia Community &amp; GAMe 2017

written 12 months ago by Galaxy News

Today we officially launch the Galaxy Australia community with the opening of registrations for the Galaxy Australasia Meeting 2017 (GAMe 2017) being held in Melbourne over 3-9 February. Australian Galaxy users and administrators will now have more opportunities to interact and collaborate to identify and address the needs of the local community. The community will also be a hub for Australian Galaxy training courses and offer a catalog of Australian Galaxy servers. The establishment of Galaxy Australia is supported by the EMBL Australia Bioinformatics Resource (EMBL-ABR) in its appointed role of supporting the development of skills and training in the Australian life science research community. At the EMBL-ABR Hub, hosted at the Victorian Life Sciences Computation Initiative (VLSCI), Galaxy is used extensively for teaching and data analysis directly as well as through the Australian-made Genomics Virtual Laboratory. VLSCI’s expert bioinformaticians and professional staff will help promote community activities and training. Galaxy Australia has a has a Twitter feed (@GalaxyAustralia) for announcements and discussion relevant to the community. Galaxy Australasia Meeting 2017 (GAMe 2017) The Community’s first major activity is to organise the Galaxy Australasia Meeting 2017 (GAMe 2017), 3-9 February in Melbourne. We are pleased to announce that early registration and talk and poster abstract submission are now open for GAMe 2017. This meeting will bring together biomedical researchers, bioinformaticians, infrastructure providers, and data producers from across Australia and Asia to share expertise across many levels. The conference starts 4 February and features two full days of keynotes, accepted and ...

October 2016 Galactic News

written 12 months ago by Galaxy News

The October Galaxy News is hot off the presses and upcoming events are prominent: Galaxy training contribution fest: October 6-7, Online Swiss-German Galaxy Days: October 20-21, Freiburg, Germany Galaxy &amp; Hacktoberfest: Month of October, online Bioconda Contribution Fest: November 2-3, Online Galaxy Admin Training: November 7-11, Salt Lake City, Utah. On time registration ends October 16 Galaxy Australasia Meeting (GAMe 2017): February 3-9, Melbourne, Victoria, Australia. Registration and abstract submission are now open. And of course, other upcoming events too There are also 117 new publications (including six featured pubs), four open positions, two new public Galaxy servers and one new semi-public Galaxy service, new releases of galaxy-lib &amp; Planemo, new TooShed contributions, and other news too. We hope to see you in Freiburg, Salt Lake, Melbourne, online, and around the world, Dave Clements and the Galaxy Team Posted to the Galaxy News on 2016-10-03-- Delivered by Feed43 service

GCC2018 Call for Host Proposals

written 12 months ago by Galaxy News

GCC2018 needs a host! (and a logo) Hello all, The Galaxy Community Conference has been held annually since 2010. GCC2017 will be held 26-30 June in Montpellier, France. We are now seeking proposals from organizations interested in hosting GCC2018. GCC alternates every year between meeting in North America, and meeting outside North America. Hosts for GCC2018 need to be located in North America. GCC draws 200+ participants from data-intensive life science research. Participants come from around the world, from all career stages, and do research spanning the tree of life. Universities, hospitals and medical schools, research organizations, and industry are all represented, including some of the largest and most influential research organizations in the world. What do you need to host GCC2018, you ask? In approximately decreasing order of importance: Enthusiasm to plan and organize several events over several days for more than 200 people. Space for 4-6 parallel training sessions, with each space able to accommodate 25 to 75 participants. Central meeting space with capacity for 250-300 people. Affordability (or access to sponsorship funds) Nearby space for breakouts, poster sessions and sponsors. Nearby space for lunch, coffee breaks. Good wifi for all events (that's 200+ people and their devices). Space for hackathons for 2 days Easy to get to by air. Nearby, affordable housing, or easy walking distance or easy public transport from lodging options to conference facilities Close proximity to a pub and other social hubs. Hosts get copious (and enthusiastic) organizational support from Galaxy's Outreach Team (who ...

September 2016 Galactic News

written 13 months ago by Galaxy News

The September Galaxy News is out: Galaxy Admin Training early registration ends September 19 Swiss-German Galaxy Days: 20-21 October Other Upcoming Events GCC2016 presentations and training are on the Galaxy F1000 channel 75 new Papers Open positions Two new public Galaxy servers RNAcommender New releases: Galaxy v16.07 CloudBridge, Planemo, Pulsar, BioBlend and galaxy-lib TooShed Contributions And other news too. Dave Clements and the Galaxy Team Posted to the Galaxy News on 2016-09-06-- Delivered by Feed43 service

Galaxy Admin Training, Nov 7-11

written 13 months ago by Galaxy News

November 7-11, 2016 University of Utah Salt Lake City, Utah United States Registration is open We are pleased to announce that registration for Galaxy Admin Training 2016 is now open. Galaxy Admin Training 2016 is a weeklong event offering basic and advanced sessions. It is being held in Salt Lake City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16) meets in Salt Lake. Basics Session: November 7-8 This two day basics session will introduce participants to what you need to know to get a Galaxy server up and running on a standalone server. You'll also learn how to extend your Galaxy with your own tools and tools from the community, and how to define reference data in your server as well. Advanced Session: November 9-11 The three day advanced session will build on topics covered in the basics section. This session both extends those topics, such as tool definition, and adds new ones, such as working with compute clusters and heterogeneous resources. The goal of the advanced workshop is to enable Galaxy administrators to create robust, high-performance Galaxy instances that take full advantage of available tools and compute and storage resources. Register by September 19 and save up to $130 off standard registration rates (and up to $250 if you work in industry). Galaxy Admin Training 2016 is hosted by the University of Utah Center for High Performance Computing (CHPC), the Department of Biomedical Informatics and the Clinical &amp; Translational Science Biomedical Informatics Core (CCTS BMIC) at the ...

July 2016 Galaxy Release (v 16.07)

written 13 months ago by Galaxy News

The Galaxy Committers team is pleased to announce the July 2016 (v16.07) release of Galaxy. Reminders Python 2.6 is no longer supported. Details: 16.01 release announcement The Galaxy source is no longer hosted on Bitbucket. Details: 16.04 release announcement. Highlights Get Galaxy On behalf of the Galaxy Core and Contributor team (and community), Thanks for using Galaxy! Posted to the Galaxy News on 2016-08-25-- Delivered by Feed43 service

Galaxy Admin Training, Nov 7-11

written 13 months ago by Galaxy News

November 7-11, 2016 University of Utah Salt Lake City, Utah United States Registration is open We are pleased to announce that registration for Galaxy Admin Training 2016 is now open. Galaxy Admin Training 2016 is a weeklong event offering basic and advanced sessions. It is being held in Salt Lake City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16) meets in Salt Lake. Basics Session: November 7-8 This two day basics session will introduce participants to what you need to know to get a Galaxy server up and running on a standalone server. You'll also learn how to extend your Galaxy with your own tools and tools from the community, and how to define reference data in your server as well. Advanced Session: November 9-11 The three day advanced session will build on topics covered in the basics section. This session both extends those topics, such as tool definition, and adds new ones, such as working with compute clusters and heterogeneous resources. The goal of the advanced workshop is to enable Galaxy administrators to create robust, high-performance Galaxy instances that take full advantage of available tools and compute and storage resources. Register by September 19 and save up to $130 off standard registration rates (and up to $250 if you work in industry). Galaxy Admin Training 2016 is hosted by the University of Utah Center for High Performance Computing (CHPC), the Department of Biomedical Informatics and the Clinical &amp; Translational Science Biomedical Informatics Core (CCTS BMIC) at the ...

Galaxy Admin Training, Nov 7-11

written 13 months ago by Galaxy News

November 7-11, 2016 University of Utah Salt Lake City, Utah United States Registration is open We are pleased to announce that registration for Galaxy Admin Training 2016 is now open. Galaxy Admin Training 2016 is a weeklong event offering basic and advanced sessions. It is being held in Salt Lake City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16) meets in Salt Lake. Basics Session: November 7-8 This two day basics session will introduce participants to what you need to know to get a Galaxy server up and running on a standalone server. You'll also learn how to extend your Galaxy with your own tools and tools from the community, and how to define reference data in your server as well. Advanced Session: November 9-11 The three day advanced session will build on topics covered in the basics section. This session both extends those topics, such as tool definition, and adds new ones, such as working with compute clusters and heterogeneous resources. The goal of the advanced workshop is to enable Galaxy administrators to create robust, high-performance Galaxy instances that take full advantage of available tools and compute and storage resources. Register by September 19 and save up to $130 off standard registration rates (and up to $250 if you work in industry). Galaxy Admin Training 2016 is hosted by the University of Utah Center for High Performance Computing (CHPC), the Department of Biomedical Informatics and the Clinical &amp; Translational Science Biomedical Informatics Core (CCTS BMIC) at the ...

August 2016 Galactic News

written 14 months ago by Galaxy News

The August Galaxy News is out: GCC2016 presentations and training are online Galaxy Admin Training Other Upcoming Events New F1000Research Galaxy Channel 55 new Papers Open positions (hurry!) Public Galaxy Server News New community hub entries TooShed Contributions And other news too. Dave Clements and the Galaxy Team Posted to the Galaxy News on 2016-07-29-- Delivered by Feed43 service

Multi-omics Postdoc Opening

written 15 months ago by Galaxy News

A post-doctoral position is available at the University of Minnesota for development of bioinformatics tools, with a focus on applications that integrate data across ‘omics’ domains (genomics, transcriptomics, proteomics and metabolomics). A particular emphasis is in the integration of mass spectrometry (MS)-based proteomics data with other types of ‘omics’ data for applications in proteogenomics and metaproteomics. The researcher will join a successful team of developers, collaborators and users who have developed the Galaxy for proteomics (Galaxy-P) platform (see usegalaxyp.org and references). A Ph.D. in bioinformatics, computer science, analytical chemistry or closely related field is required. Experience with MS-based proteomics data analysis is highly preferred, and familiarity with the Galaxy framework is a plus. Interested applicants can apply directly to Dr. Tim Griffin &lt;tgriffin@umn.edu&gt;. Posted to the Galaxy News on 2016-07-22-- Delivered by Feed43 service

July 2016 Galactic News

written 15 months ago by Galaxy News

Some highlights from the July Galaxy News: GCC2016 is done! and slides and posters are now online (and video and training materials are coming) And there is plenty more happening: GCC2017 Announced! Swiss-German Galaxy Days Galaxy Admin Training announced European Galaxy Developer Knowledge Exchange Galaxy AustralAsia Meeting (GAMe 2017) announced Other Upcoming Events 82 new Papers Open positions New public and semi-public Galaxy servers A new community log board entry New Releases: blend4php, Planemo, and galaxy-lib And other news too. Hope to see you in Montpellier! Dave Clements and the Galaxy Team Posted to the Galaxy News on 2016-07-06-- Delivered by Feed43 service

June 2016 Galactic News

written 16 months ago by Galaxy News

Some highlights from the June Galaxy News GCC2016 News Complete schedule is online Register by June 4 You can still submit a poster GCC2016 Opening Reception added Please welcome new GCC sponsor: Bloomington Life Sciences Partnership. Other Upcoming Events: Using Galaxy for Analysis of RNA-Seq and ChIP-Seq Data Workshop @ UC Davis GalaxyAdmins June Meetups All June, July, and August Events Papers (76 of them, 4 highlighted) Open positions (5 of them) New Semi-Public Galaxy Servers Directory and new Commercial Support Directory A new Galaxy Trainer New Releases: Galaxy v16.04, CloudMan 16.04, Planemo, and galaxy-lib. April and May ToolShed Contributions, and other news too. Hope to see you in Bloomington, Dave Clements and the Galaxy Team Posted to the Galaxy News on 2016-06-01-- Delivered by Feed43 service

April 2016 Galaxy Release (v 16.04)

written 16 months ago by Galaxy News

The Galaxy Committers team is pleased to announce the April 2016 (v16.04) release of Galaxy. Please note that Python 2.6 is no longer supported as of this release. See the 16.04 release announcement for details. Highlights Tool Profile Versions Tools may now declare which version of Galaxy they require. Tools requiring 16.04 or newer will have new default behaviors (such as using exit code for error detection) that should simplify tool development. See PR #1688. Embedded Pulsar Job Runner Galaxy can now start a Pulsar application embedded within the Galaxy process itself. This allows using Pulsar’s job staging and isolation without requiring a RESTful web service or a message queue. This is enabling usegalaxy.org to run jobs to on the new JetStream cloud. See PR #2057. New Chemical Datatypes Galaxy now detects and supports many molecular datatypes. See PR 1941. Thanks to Björn Grüning (@bgruening). Github New % git clone -b master https://github.com/galaxyproject/galaxy.git Update to latest stable release % git checkout master &amp;&amp; git pull --ff-only origin master Update to exact version % git checkout v16.04 BitBucket Upgrade % hg pull % hg update latest_16.04 See the Get Galaxy page for additional details regarding the source code locations. Thanks for using Galaxy! Posted to the Galaxy News on 2016-05-18-- Delivered by Feed43 service

16.05 Galaxy CloudMan release

written 17 months ago by Galaxy News

We just released an update to Galaxy CloudMan on AWS. CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration or imposed quotas. Once running, you have complete control over Galaxy, including the ability to install new tools. This is a minor update release with the following changes: Galaxy 16.04 update Availability on Amazon's Ireland region A couple of bug fixes See the CHANGELOG for a more complete set of changes. Posted to the Galaxy News on 2016-05-25-- Delivered by Feed43 service

April 2016 Galaxy Release (v 16.04)

written 17 months ago by Galaxy News

The Galaxy Committers team is pleased to announce the April 2016 (v16.04) release of Galaxy. Please note that Python 2.6 is no longer supported as of this release. See the 16.04 release announcement for details. Highlights Tool Profile Versions Tools may now declare which version of Galaxy they require. Tools requiring 16.04 or newer will have new default behaviors (such as using exit code for error detection) that should simplify tool development. See PR #1688. Embedded Pulsar Job Runner Galaxy can now start a Pulsar application embedded within the Galaxy process itself. This allows using Pulsar’s job staging and isolation without requiring a RESTful web service or a message queue. This is enabling usegalaxy.org to run jobs to on the new [[|http://jetstream-cloud.org/|JetStream cloud]]. See PR #2057. New Chemical Datatypes Galaxy now detects and supports many molecular datatypes. See PR 1941. Thanks to Björn Grüning (@bgruening). Github New % git clone -b master https://github.com/galaxyproject/galaxy.git Update to latest stable release % git checkout master &amp;&amp; git pull --ff-only origin master Update to exact version % git checkout v16.04 BitBucket Upgrade % hg pull % hg update latest_16.04 See the Get Galaxy page for additional details regarding the source code locations. Thanks for using Galaxy! Posted to the Galaxy News on 2016-05-18-- Delivered by Feed43 service

April 2016 Galaxy Release (v 16.04)

written 17 months ago by Galaxy News

The Galaxy Committers team is pleased to announce the April 2016 (v16.04) release of Galaxy. Please note that Python 2.6 is no longer supported as of this release. See the 16.04 release announcement for details. Highlights Tool Profile Versions Tools may now declare which version of Galaxy they require. Tools requiring 16.04 or newer will have new default behaviors (such as using exit code for error detection) that should simplify tool development. See PR #1688. Embedded Pulsar Job Runner Galaxy can now start a Pulsar application embedded within the Galaxy process itself. This allows using Pulsar’s job staging and isolation without requiring a RESTful web service or a message queue. This is enabling usegalaxy.org to run jobs to on the new [[|http://jetstream-cloud.org/|JetStream cloud]]. See PR #2057. New Chemical Datatypes Galaxy now detects and supports many molecular datatypes. See PR 1941. Thanks to Björn Grüning (@bgruening). Github New % git clone -b master https://github.com/galaxyproject/galaxy.git Update to latest stable release % git checkout master &amp;&amp; pull --ff-only origin master Update to exact version % git checkout v16.04 BitBucket Upgrade % hg pull % hg update latest_16.04 See the Get Galaxy page for additional details regarding the source code locations. Thanks for using Galaxy! Posted to the Galaxy News on 2016-05-18-- Delivered by Feed43 service

May 2016 Galactic News

written 17 months ago by Galaxy News

Some highlights from the May Galaxy News GCC2016 Deadlines! and Sponsors Poster &amp; Demo Abstracts: May 20 Early Registration: May 20 Scholarships: May 1 Please welcome returning GCC sponsors: GigaScience, GenomeWeb, and EMC. Other Upcoming Events: Galaxy @ ASMS 2016 Using Galaxy for Analysis of RNA-Seq and ChIP-Seq Data Workshop @ UC Davis All May, June and July Events Galaxy on Jetstream Cloud New tutorials and video on Diploid Variant Calling, Reference Based RNA-Seq, and Dataset Collections. Slides and video from the April GalaxyAdmins meetup and a report from the Conda Dependency Codefest Papers (72 of them, 8 highlighted) Open positions (6 of them) New MGEScan and Koslicki Lab public Galaxy servers A new Galaxy Community Hub training resource New Releases: Planemo, and galaxy-lib and Pulsar Don't miss those deadlines, and see you in June, Dave Clements and the Galaxy Team Posted to the Galaxy News on 2016-04-29-- Delivered by Feed43 service

Conda Dependencies Codefest Report

written 18 months ago by Galaxy News

The codefest started via hangouts at 10am EDT on Monday April 4, with around 8 participants. It was designed to be beginner friendly, which increased contribution from the community. 4 members of the galaxy community were added as contributors to the bioconda-recipe repository as a result of this hackathon. The codefest started with Björn Grüning giving a small introduction to Conda and its channel Bioconda. Followed by how to create a new Conda recipe and the scripts involved in it. Members of the hack started by then picking up a simple tool and creating a Pull request against both the Tools-IUC and bioconda-recipes repositories on GitHub. The main aim of the codefest was to get community members familiar with the Conda-Galaxy integration, and to remove tools from testing blacklist (shown below). More details are here. List of tools (versions) added to Bioconda: Seqtk r-75 Shaker EDirect PeptideShaker and SearchGUI OpenBabel BamHash Trf List of tools in [WIP]: All perl packages on osx Bioconductor minfi List of tools removed from .tt_blacklist in IUC Seqtk Vegan Art Macs2 Infrastructure: Automatic push from tested tools to the Test Tool Shed in tools-iuc and bgruenings galaxytools More strict dependency handling in Bioconda Thanks to everyone who participated! Rémi Marenco. Nitesh Turaga, and Björn Grüning Posted to the Galaxy News on 2016-04-07-- Delivered by Feed43 service
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Galaxy Events Calendar
The Galaxy Events calendar lists any events that the Galaxy Project knows about that may be of interest to the Galaxy community. The event does not have to feature Galaxy in any way. For only events that feature Galaxy, see the Galaxy Events page at https://wiki.galaxyproject.org/Events.
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