
===========================================================
January 2020 Galaxy Release (v 20.01)
===========================================================

.. include:: _header.rst

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

**Workflow Executions Menu**
  This menu can be reached from the User menu -> Workflow Invocations
  and lists your recent Workflow executions, their status and links
  to the Workflow Editor and the History with the results of the
  Workflow run.

.. figure:: https://user-images.githubusercontent.com/216771/65520097-0a041f80-deb5-11e9-80ac-2557b36c252f.png
   :alt: Workflow invocation menu
   :width: 400px

.. figure:: https://user-images.githubusercontent.com/6804901/73737075-345ac900-4742-11ea-9f50-0f0e4c3d9271.png
   :alt: Workflow invocatios

**Galay Markdown Pages and Workflow Reports as PDF**
  An additional link has been added to Galaxy Markdown Pages and Workflow reports
  that exports your document as a standalone PDF.

.. figure:: https://user-images.githubusercontent.com/6804901/73776256-b7524280-4787-11ea-821f-d9a8c6339ee9.png
   :alt: Example PDF export

**Screenreader-friendly Navigation**
  The top menu and the Workflow Editor have been improved for easier navigation
  using Screenreaders and the Keyboard.
  Thanks goes to `@WilliamHolden  <https://github.com/WilliamHolden>`__

**Email-notification for completed jobs**
  You can now select to be notified by email when a tool run has finished.
  Thanks goes to `@astrovsky01 <https://github.com/astrovsky01>`__

.. figure:: https://user-images.githubusercontent.com/6804901/73779180-a2c47900-478c-11ea-98ab-7355276b6f6d.png
   :alt: Example of email button
   :width: 300px

New Visualizations
===========================================================

.. visualizations

* Add data dialog input element to client form parameter list
  `Pull Request 8774`_
* Wrap SQL statement in a text() function as required by sqlalchemy
  (thanks to `@kaukrise <https://github.com/kaukrise>`__).
  `Pull Request 9216`_
* Ensure visible overflow on navbar container
  (thanks to `@kaukrise <https://github.com/kaukrise>`__).
  `Pull Request 9217`_

New Datatypes
===========================================================

.. datatypes

* Datatypes for MassSpec DIA dlib,elib
  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
  `Pull Request 8657`_
* Add bus as binary, remove extra datatype
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 8705`_
* remove dada2_derep data type
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 8902`_
* Add new GROMACS datatypes: ndx, xvg, edr
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 8964`_
* add gff3.gz and gff3.bz2 datatypes
  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
  `Pull Request 8967`_
* Make mol2 visible
  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
  `Pull Request 8995`_
* Add a datatype subclass for CAT (Contig Annotation Tool)
  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
  `Pull Request 9087`_
* Fix cool sniffing on python3
  `Pull Request 9153`_
* Allow tabular.gz / add embl to uploadable formats
  `Pull Request 9293`_

Builtin Tool Updates
===========================================================

.. tools

* Upgrade askomics interactive tool
  (thanks to `@xgaia <https://github.com/xgaia>`__).
  `Pull Request 8517`_
* Remove collection ID character restriction from 'Relabel collection from file' tool
  (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
  `Pull Request 8571`_
* Allow space, dot and comma in relabel identifier tool
  `Pull Request 8757`_
* Fix script shebangs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 8888`_
* grouping: strip newlines
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 8953`_
* Allow admins to import tools/workflows from paths.
  `Pull Request 9003`_
* Add requirements to interval_to_bed_converter.xml
  `Pull Request 9041`_
* Move sam_pileup to GALAXY_LIB_TOOLS_VERSIONED
  `Pull Request 9320`_
* Add requirements, fix legacy tools and move them out of GALAXY_LIB_TOOLS_UNVERSIONED
  `Pull Request 9336`_
* Add requirements to (almost) all converters, profile and minor fixes
  `Pull Request 9345`_
* Fix version in which ``sam_pileup`` was fixed
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9350`_
* Expunge tool shed repository objects, prevents ParentInstanceDetachedError
  `Pull Request 9354`_
* Remove GenomeSpace tools, OpenID, UI and requirements
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9363`_
* Fix maf tools
  `Pull Request 9393`_
* XML fix for joiner.xml.
  `Pull Request 9399`_

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

Please see the :doc:`full release notes <20.01_announce>` for more details.

.. include:: 20.01_prs.rst

.. include:: _thanks.rst
