Galaxy Wiki
Galaxy Development News Briefs describe new Galaxy releases, and what has happened in the code since the previous release. Each release is summarized here, and gets its own Development News Brief page. Older Development News Briefs can be found in the Development News Brief Archive.
See also
Complete News Brief
Highlights:
Emboss tools and datatypes have now moved from the Galaxy distribution to the Galaxy Main Tool Shed.
Tool Integration Tests, Custom Tool Panel Configuration, and Configurable Tool Output Locations.
Improved Multiprocess Job Handling and Enhanced OpenID Support.
GATK version 1.4, FreeBayes, Updated Megablast using NCBI BLAST+, Trinity, WormBase 2, and IGB external display.
Trackster upgrades include strand coloring, interval datatype support, and tabix indexing (fast!!).
Updated User Interface, Workflow-API upgrades, and Custom UCSC Display.
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 17d57db9a7c0
Thanks for using Galaxy!
Complete News Brief
Highlights:
Emboss tools and datatypes moving from the Galaxy distribution to the Galaxy's Main Tool Shed in the NEXT release. Read more about the upcoming tool migrations...
Galaxy tool XML configuration, managing tool panel layout, and Galaxy tool versions.
RNA-Seq Tools: Added CuffMerge version 1.0.0, Updated TopHat default parameters
Now visualize ENCODE "peak" datatype tracks in the Galaxy Track Browser (aka Trackster)
Multiple Workflow updates including enhancements to input dataset options, display modes, and sharing.
CloudMan now offers preliminary support for OpenNebula cloud type and a larger default tools volume (10GB vs old 2GB).
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 40f1816d6857
Thanks for using Galaxy!
Complete News Brief
Highlights:
- Important metadata and Python 2.5 support corrections
Dynamic filtering, easy color options, and quicker indexing enhance Trackster
Set up your Galaxy instance to run cluster jobs as the real user, not the Galaxy owner
Improvements to metadata handling and searching in the Tool Shed
Improved solutions for schema access, jobs management, & workflow imports and inputs.
- New datatypes (Eland, XML), multiple tool enhancements, and bug fixes.
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 26920e20157f
Thanks for using Galaxy!
Complete News Brief
Highlights:
- New Object Store data integration layer introduced
RNA-seq updates: TopHat to 1.4.0 and Cufflinks, CuffDiff, & CuffCompare to 1.3.0.
- Tool Shed installation features and many new community tool additions
Trackster performance upgrades and new drag & drop composite track creation
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 63bc46cc73b7
Thanks for using Galaxy!
Complete News Brief
Highlights:
GCC2012 is Scheduled! We are pleased to announce that the 2012 Galaxy Community Conference (GCC2012) has been scheduled for July 25-27 in Chicago, Illinois, United States.
Galaxy tool sheds play a beneficial role in enabling sharing of workflows & tools
New wrappers, new tool upgrades: Python, FASTQC, Picard, TopHat
Direct Galaxy dataset link to browse VCF and BAM files in the Integrative Genomics Viewer (IGV)
- New Trackster features, UI and Source updates, Bug fixes
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r b258de1e6cea
Thanks for using Galaxy!
Complete News Brief
Highlights:
Main Public server at http://usegalaxy.org implements data & job quotas
- User Interface updates and new features for managing data and more
Trackster (aka Galaxy Track Browser or GTB) at BioVis, too many new features to list out, try it!
- It's official, Python 2.7 is the standard and 2.4 is deprecated
- Smooth new Tool Shed functions make setting up a local Galaxy even easier (and it was pretty easy already)
- Source updates, bug fixes, new scripts, wrapped tools, and custom tools
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 338ead4737ba
Thanks for using Galaxy!
Complete News Brief
Highlights:
- An improved Galaxy Tool Shed for sharing tool definitions
- New or updated tool definitions for Trinity, BWA, FASTQ Groomer, Cufflinks, Cuffdiff, amd Cuffcompare
- Data visualization enhancements including bookmarking genomic regions, overview tracks, and increased user control
- Better cloning of workflows, and uploading to myExperiment.
- API improvements for managing histories and datasets, including creating histories from library items.
new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 949e4f5fa03a
Thanks for using Galaxy!
