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76 lines
4.1 KiB
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76 lines
4.1 KiB
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===========================================================
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January 2017 Galaxy Release (v 17.01)
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===========================================================
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.. include:: _header.rst
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Highlights
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===========================================================
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**Conda auto initialization is enabled by default**
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After updating to 17.01 and upon starting Galaxy the Conda package manager will be installed automatically
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within the Galaxy's workspace. This will enable your Galaxy to install tool dependencies from Conda channels
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such as `BioConda <https://bioconda.github.io/>`__. Such channels are already being used for new and updated tools by IUC
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and we suggest adopting this tool dependency resolution method to all tool developers instead of Tool Shed package
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recipes - which are now considered deprecated.
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Please see the details at the admin :doc:`documentation <../admin/conda_faq>`.
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**New interface for user preferences**
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User preferences menu has been reworked for clarity and consistency.
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Thanks to `@anuprulez <https://github.com/anuprulez>`__ and `@bgruening <https://github.com/bgruening>`__.
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Implemented in `Pull Request 3118`_.
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**Support for compressed FASTQ formats**
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You can now upload compressed (with gzip or bzip2) FASTQ files without them being unpacked automatically (as it was until now).
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For this to work you have to select the proper type when uploading (e.g. instead of ``fastqsanger`` you select ``fastqsanger.gz``
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or ``fastqsanger.bz2`` for compressed files).
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Existing tools will work as before and future tools will be able to consume archives and save space in your quota.
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Thanks to `@abretaud <https://github.com/abretaud>`__, `@ashvark <https://github.com/ashvark>`__, `@jvolkening <https://github.com/jvolkening>`__, and `@mvdbeek <https://github.com/mvdbeek>`__.
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Implemented in `Pull Request 3145`_, `Pull Request 3510`_ and `Pull Request 3514`_.
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Get Galaxy
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==========
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The code lives at `Github <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
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To get a new Galaxy repository run:
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.. code-block:: shell
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$ git clone -b release_17.01 https://github.com/galaxyproject/galaxy.git
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To update an existing Galaxy repository run:
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.. code-block:: shell
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$ git checkout release_17.01 && git pull --ff-only origin release_17.01
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See `our wiki <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
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Deprecation Notices
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===================
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* Galaxy tools no longer have access to Galaxy's core framework Python code during tool execution - see
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`Pull Request 3364`_ for implementation details.
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Previously, Galaxy's ``lib`` directory would be placed on a tool's PYTHONPATH - but this can cause different sorts of
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conflicts with resolved dependencies and should never really have been part of the interface exposed to tools since
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it makes both reproducibility and distribution of jobs difficult.
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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`_
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and we will continue to add there if we find more. If you discover a tool that has problems importing e.g. ``galaxy`` or
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``galaxy_utils`` as a result of this release please let us know by `creating an issue
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<https://github.com/galaxyproject/galaxy/issues/new>`__ with a link to the Tool Shed page of the tool.
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If you have local tools that depend on these modules and you do not wish to use a formal dependency resolution mechanism
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such as Conda, you can change the option ``preserve_python_environment`` in galaxy.ini from ``legacy`` to ``legacy_and_local``.
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* 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>`__.
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Release Notes
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===========================================================
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.. include:: 17.01.rst
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:start-after: announce_start
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.. include:: _thanks.rst
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