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January 2017 Galaxy Release (v 17.01)

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Highlights

Conda auto initialization is enabled by default

After updating to 17.01 and upon starting Galaxy the Conda package manager will be installed automatically within the Galaxy’s workspace. This will enable your Galaxy to install tool dependencies from Conda channels such as BioConda. Such channels are already being used for new and updated tools by IUC and we suggest adopting this tool dependency resolution method to all tool developers instead of Tool Shed package recipes - which are now considered deprecated. Please see the details at the admin documentation.

New interface for user preferences

User preferences menu has been reworked for clarity and consistency. Thanks to @anuprulez and @bgruening. Implemented in Pull Request 3118.

Support for compressed FASTQ formats

You can now upload compressed (with gzip or bzip2) FASTQ files without them being unpacked automatically (as it was until now). For this to work you have to select the proper type when uploading (e.g. instead of fastqsanger you select fastqsanger.gz or fastqsanger.bz2 for compressed files). Existing tools will work as before and future tools will be able to consume archives and save space in your quota. Thanks to @abretaud, @ashvark, @jvolkening, and @mvdbeek. Implemented in Pull Request 3145, Pull Request 3510 and Pull Request 3514.

Get Galaxy

The code lives at Github and you should have Git to obtain it.

To get a new Galaxy repository run:
$ git clone -b release_17.01 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git checkout release_17.01 && git pull --ff-only origin release_17.01

See our wiki for additional details regarding the source code locations.

Deprecation Notices

  • Galaxy tools no longer have access to Galaxy’s core framework Python code during tool execution - see Pull Request 3364 for implementation details.

    Previously, Galaxy’s lib directory would be placed on a tool’s PYTHONPATH - but this can cause different sorts of conflicts with resolved dependencies and should never really have been part of the interface exposed to tools since it makes both reproducibility and distribution of jobs difficult.

    Unfortunately, there is a large number of Galaxy tools - both in the core distribution and in the Tool Shed - that depend on Galaxy internals. The ones we know about have been added to a whitelist as part of Pull Request 3364 and we will continue to add there if we find more. If you discover a tool that has problems importing e.g. galaxy or galaxy_utils as a result of this release please let us know by creating an issue with a link to the Tool Shed page of the tool.

    If you have local tools that depend on these modules and you do not wish to use a formal dependency resolution mechanism such as Conda, you can change the option preserve_python_environment in galaxy.ini from legacy to legacy_and_local.

  • Galaxy’s ‘repair repository’ feature for installed repositories is deprecated and will be removed/replaced in the next release - details.

Release Notes

Enhancements

Fixes

To stay up to date with Galaxy’s progress watch our screencasts, visit our community hub, and follow @galaxyproject on Twitter.

You can always reach us on Gitter or IRC.

Thanks for using Galaxy!

The Galaxy Team