
===========================================================
May 2018 Galaxy Release (v 18.05)
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.. include:: _header.rst

Highlights
===========================================================

**New Interface Style Library**
  The design of many components of the Galaxy user interface has been subtly improved as the result
  of upgrading to the Bootstrap 4 style library. The upgrade process was a large community effort
  with commits from six contributors and testing and bug reports from many others. A huge
  thanks goes out to everyone who helped - it is a great step forward toward a more
  standardized Galaxy client infrastructure built on reactive `VueJS <https://vuejs.org/>`__
  components. Read more about whats new and changed in the underlying Bootstrap 4 JavaScript
  library `here <http://blog.getbootstrap.com/2018/01/18/bootstrap-4/>`__.

  `Pull Request 5807`_, `Galaxy Project Board for Bootstrap 4
  <https://github.com/galaxyproject/galaxy/projects/10>`__.

**Unlimited Browser Upload Size**
  Support for chunked and resumable file uploads out-of-the-box. This should effectively
  eliminate browser-based limitations on the size of files that can be uploaded to Galaxy.

  `Pull Request 5516`_

**New Powerful Rule-Based Data Uploader**
  Galaxy now features a powerful new interface for manipulating lists of rules for processing metadata
  that can be used to describe the upload of arbitrarily complex collections as well as individual
  datasets. These rules can be used to build collections from lists of URLs, FTP directory contents,
  data library folders, and tabular sample sheets or exports from external data sources. The same
  technique can be applied to the metadata of an existing collection, enabling very flexible
  filtering, sorting, relabelling, grouping, flattening, and general re-organization of collections.
  This client widget is backed by a powerful new `hierarchical upload API <https://github.com/galaxyproject/galaxy/pull/5220>`__
  and `a new collection operation tool <https://github.com/galaxyproject/galaxy/pull/5819>`__.

  Check out `this tutorial <https://github.com/jmchilton/training-material/blob/rules/topics/introduction/tutorials/galaxy-intro-rules/tutorial.md>`__ describing new techniques for loading
  large numbers of datasets and complex collections into Galaxy.

  `Pull Request 5365`_, `Pull Request 5220`_, `Pull Request 5819`_, `Pull Request 5823`_,
  `Pull Request 5929`_, `Pull Request 5940`_

**GDPR Beta Mode**
  We introduce beta GDPR privacy mode. Admins can enable it to help them comply with the European Union law
  known as `General Data Protection Regulation <http://eur-lex.europa.eu/legal-content/en/TXT/?uri=CELEX:32016R0679>`__,
  which goes into effect on May 25, 2018. Thanks to `@hexylena <https://github.com/hexylena>`__.

  `Pull Request 6069`_

**New HIV-TRACE Plugin**
  Integration of a new visualization plugin - HIV-TRACE. Thanks to `@veg <https://github.com/veg>`__!

  `Pull Request 5869`_

**Visualization Frameworks Unified**
  The charts and generic visualization frameworks have been merged together into a single coherent
  one. You can use a new menu option to list and search all available visualizations.

  `Pull Request 5633`_, `Pull Request 5505`_

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_18.05 https://github.com/galaxyproject/galaxy.git

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

      $ git fetch origin && git checkout release_18.05 && git pull --ff-only origin release_18.05

See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.

Security
========

vcffilter by devteam allowed RCE
--------------------------------
Tracked as ``GX-2018-0004``.

Older versions of the VCF filter tool in the `vcffilter repository by devteam <https://toolshed.g2.bx.psu.edu/view/devteam/vcffilter/>`__ allowed remote code execution due to missing character escaping.
If you have this repository installed in your Galaxy, please update to the revision ``4:6b935ab36d7b`` or newer and disable/uninstall all older versions.

Breaking Changes
================

* The ``charts`` repository that powers Galaxy built-in visualizations that need backend computation has been moved to the IUC account. In order for these visualization options to keep working, admins need to install the following repository: `iuc/charts <https://toolshed.g2.bx.psu.edu/view/iuc/charts/>`__.

* Removed support for the Graphite statistics middleware. We continue to further support the ``statsd`` middleware.

* We reworked how compressed archives (zip, gz, bz etc.) are being defined and handled in Galaxy. As a result, if you have a custom ``datatypes_conf.xml`` configuration file, you should remove the compressed sniffers that used to be in the sample file but `now are not <https://github.com/galaxyproject/galaxy/blob/release_18.05/config/datatypes_conf.xml.sample>`__. Otherwise you will encounter non-breaking errors in the logs.

* We have removed the deprecated symlink `static/scripts/packed -> .` If you used it please change your (proxy) configuration. An example can be seen `here <https://github.com/galaxyproject/ansible-galaxy-extras/pull/206/files>`__.

Release Notes
=============

.. include:: 18.05.rst
   :start-after: announce_start

.. include:: _thanks.rst
