new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r ec29ce8e27a1
The 2012 Galaxy Community Conference (GCC2012) is a few short days away. Late registration is still open.
FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.
The emboss_5 repository in the Galaxy Main Tool Shed has been updated to include information for automatically installing the EMBOSS Version 5.0.0 tool dependencies. If you've installed the emboss_5 repository into your local Galaxy instance, get this update from the tool shed, and you'll have the option of installing the tool dependencies.
Admin Genome Indexing
If enable_beta_job_managers = True, Galaxy will now show a new option in the admin interface, titled Manage Local Data. With this tool, a Galaxy admin will be able to select and download any genome already contained with the local $GALAXYROOT/tool-data/shared/ucsc/builds.txt file sourced from UCSC, NCBI, or Ensembl, optionally indexing the FASTA data with one or more of BWA, Bowtie, Bowtie 2, PerM, Picard, and SAM. After these processes finish, the indexed build will then be available for other tools in the analysis section. This does not replace setting up a build.txt file (read more ...). This would replace many of the manual indexing processes for commonly used tools (read more...). Please this tool is still beta, feedback and bug reports welcome at firstname.lastname@example.org for discussion. We will also touch on it during a breakout session at GCC (Day 2, Section 8, Automation Strategies).
Example of selecting a source, the indexes to create, and the target genome:
The status of the indexing for a single genome:
And a global status of all indexes for all genomes in progress:
Simplified install of 3rd-party Dependencies
Automatic third-party tool dependency installation and compilation with installed repositories
Tool shed repository owners can define information in their repositories that enable third party tool dependencies to be automatically installed along with the repository for those repositories that contain tools that require the dependencies. The process for enabling this is the inclusion of a simple xml file named tool_dependencies.xml in the repository. Read more…
Improved Error Handling
Several changes made in in determining errors from tool exit codes and output. In the past, Galaxy has determined if a tool has an error by checking if anything was written to standard error (stderr}). Now each tool's XML can be customized to check the tool's exit code, standard output (stdout), and standard error (stderr). The exit code can be checked against a supplied range of values, and regular expressions can be checked against stdout and stderr. Users can specify if the error should result in a warning or a fatal error. If this feature is not specified, then the previous behavior of just checking stderr will be used.
Tophat2 wrapper enhancements:
use Bowtie2 build
- add option to report discordant pairs
- update tests
add Bowtie2 preset options
User Interface (UI)
Full integration with myExperiment website. Galaxy workflows can be
exported from Galaxy to myExperiment and
- searched and imported from myExperiment website
- Support for genomes as first-class objects
Galaxy Track Browser (GTB)
- New parameter space visualization for Trackster
- Make bookmarks available in shared Trackster visualizations
- The tool shed's category grid is now displayed when searching and browsing tool sheds from a local Galaxy instance.
- This category grid's search feature searches valid repository names and descriptions when browsing a tool shed from Galaxy.
- Going forward from this Galaxy release, the main Galaxy tool shed will track the Galaxy releases and the galaxy-dist repository on bitbucket.
- Support Unvalidated values when exporting histories
The new RGalaxy package in Bioconductor. Read more …
GalaxyCzarsGalaxyCzars group was launched and had its first meetup on July 9. GalaxyCzars is a group of people that manage large local Galaxy installations. See the meeting writeup for links to slides and a screencast. The GalaxyCzars will have a breakout at GCC2012, and the next conference call will follow in September.
Galaxy is Hiring!
Want to work on one of the fastest growing open source bioinformatics projects around? The Galaxy Project, a highly successful high throughput data analysis platform for Life Sciences with over 15,000 users worldwide, is hiring. Read more...