
===========================================================
January 2017 Galaxy Release (v 17.01)
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.. include:: _header.rst

Highlights
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**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 <https://bioconda.github.io/>`__. 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 :doc:`documentation <../admin/conda_faq>`.

**New interface for user preferences**
  User preferences menu has been reworked for clarity and consistency.
  Thanks to `@anuprulez <https://github.com/anuprulez>`__ and `@bgruening <https://github.com/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 <https://github.com/abretaud>`__, `@ashvark <https://github.com/ashvark>`__, `@jvolkening <https://github.com/jvolkening>`__, and `@mvdbeek <https://github.com/mvdbeek>`__.
  Implemented in `Pull Request 3145`_, `Pull Request 3510`_ and `Pull Request 3514`_.

Get Galaxy
==========

The code lives at `Github <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.

To get a new Galaxy repository run:
  .. code-block:: shell

      $ git clone -b release_17.01 https://github.com/galaxyproject/galaxy.git

To update an existing Galaxy repository run:
  .. code-block:: shell

      $ git checkout release_17.01 && git pull --ff-only origin release_17.01

See `our wiki <https://galaxyproject.org/develop/source-code/>`__ 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
  <https://github.com/galaxyproject/galaxy/issues/new>`__ 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 <https://github.com/galaxyproject/galaxy/issues/2929>`__.

Release Notes
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.. include:: 17.01.rst
   :start-after: announce_start

.. include:: _thanks.rst
