May 2017 Galaxy Release (v 17.05)

Get Galaxy

Highlights

Tag your data with propagating hashtags

Large Galaxy histories used to be messy. Hashtags make it easy to track dataset (and collection) relationships. These two movies (both under a minute) explain how to use this with datasets and with collections.

Learn more about Galaxy histories in our updated tutorial

Drag & Drop datasets into tool inputs

Interface now allows dragging datasets from history panel into the content selectors of the tool form. Implemented in Pull Request 3871.

Upload directly to a collection

You can now bypass the history manipulation and upload your data straight into a collection for convenience.

Learn more about collections and how to use them in a new tutorial.

We extend special thanks to the 64 New Contributors to Galaxy in the past year.

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_17.05 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git checkout release_17.05 && git pull --ff-only origin release_17.05

See the community hub for additional details regarding the source code locations.

Additionaly there are New Configuration Options and New Datatypes sections.

Release Notes

Enhancements

Fixes

New Contributors

We thank these new contributors that helped with the Galaxy codebase since 16.04:

  • Evgeny Anatskiy

  • Abdulrahman Azab

  • balto

  • Bérénice Batut

  • Marius van den Beek

  • Maria Bernard

  • Jean-Frédéric Berthelot

  • Léo Biscassi

  • Clemens Blank

  • Jorrit Boekel

  • Christian Y. Brenninkmeijer

  • Freek de Bruijn

  • Matt Chambers

  • Peter Cock

  • Matthias Desmet

  • Shane Dowling

  • Ignacio Eguinoa

  • Mark Einon

  • fescudie

  • Anne Fouilloux

  • Jean-Frédéric

  • Maximilian Friedersdorff

  • Ben Fulton

  • Carrie Ganote

  • Ryan Golhar

  • Peter van Heusden

  • Saskia Hiltemann

  • Hans-Rudolf Hotz

  • Manabu Ishii

  • Xiaoqian Jiang

  • Iyad Kandalaft

  • Edward Kirton

  • Jasper Koehorst

  • Anup Kumar

  • Delphine Lariviere

  • Yvan Le Bras

  • Gildas Le Corguillé

  • Alexander Lenail

  • Pierre Lindenbaum

  • Mikael Loaec

  • Thoba Lose

  • Zipho Mashologu

  • Hervé Ménager

  • Pablo Moreno

  • Takao Nakaguchi

  • Balthazar Pavot

  • Matt Ralston

  • ramezrawas

  • Athos Ribeiro

  • Devon Ryan

  • Michael Sauria

  • Varun Shankar

  • Timur Shtatland

  • Sourav Singh

  • Eteri Sokhoyan

  • Nick Stoler

  • Scott Szakonyi

  • Jesse c j van Dam

  • Ashok Varadharajan

  • Jeremy Volkening

  • Pavan Videm

  • Junzhou Wang

  • Joachim Wolff

  • Thomas Wollmann

  • Jay Young

New Configuration Options

Below are the newly added options you can configure in galaxy.ini. To see the whole sample file visit our GitHub repository.

# Set to True to enable monitoring of the tool_data and shed_tool_data_path
# directories. If changes in tool data table files are found, the tool data
# tables for that data manager are automatically reloaded.
# Watchdog ( https://pypi.python.org/pypi/watchdog ) must be installed and
# available to Galaxy to use this option. Other options include 'auto'
# which will attempt to use the watchdog library if it is available but won't
# fail to load Galaxy if it is not and 'polling' which will use a less
# efficient monitoring scheme that may work in wider range of scenarios
# than the watchdog default.
#watch_tool_data_dir = False

# To run interactive environment containers in Docker Swarm mode (on an
# existing swarm), set this option to True and set `docker_connect_port` in the
# IE plugin config (ini) file(s) of any IE plugins you have enabled and ensure
# that you are not using any `docker run`-specific options in your plugins'
# `command_inject` options (swarm mode services run using `docker service
# create`, which has a different and more limited set of options). This option
# can be overridden on a per-plugin basis by using the `swarm_mode` option in
# the plugin's ini config file.
#interactive_environment_swarm_mode = False

# Galaxy can run a "swarm manager" service that will monitor utilization of the
# swarm and provision/deprovision worker nodes as necessary. The service has
# its own configuration file.
#swarm_manager_config_file = config/swarm_manager_conf.yml

# Log to graphite
# Graphite is an external statistics aggregator (https://github.com/graphite-project/carbon)
# Enabling the following options will cause galaxy to log request timing and
# other statistics to the configured graphite instance. The graphite_prefix is
# useful if you are running multiple Galaxy instances and want to segment
# statistics between them within the same aggregator.
#graphite_host=
#graphite_port=2003
#graphite_prefix=galaxy

# Enable the new container interface for Interactive Environments
#enable_beta_containers_interface = False

New Datatypes

Below are the newly added datatypes and sniffers you can configure in datatypes_conf.xml. To see the whole sample file visit our GitHub repository.

<datatype extension="d3_hierarchy" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
<datatype extension="mzdata" type="galaxy.datatypes.proteomics:MzData" mimetype="application/xml" display_in_upload="true" />
<datatype extension="percin" type="galaxy.datatypes.tabular:Tabular" subclass="true" />
<datatype extension="percout" type="galaxy.datatypes.xml:GenericXml" subclass="true" />
<datatype extension="hardklor" type="galaxy.datatypes.tabular:Tabular" subclass="true" />
<datatype extension="kronik" type="galaxy.datatypes.tabular:Tabular" subclass="true" />
<datatype extension="ptalign" type="galaxy.datatypes.text:PlantTribesMultipleSequenceAlignment" />
<datatype extension="ptortho" type="galaxy.datatypes.text:PlantTribesOrtho" />
<datatype extension="ptorthocs" type="galaxy.datatypes.text:PlantTribesOrthoCodingSequence" />
<datatype extension="pttree" type="galaxy.datatypes.text:PlantTribesPhylogeneticTree" />
<sniffer type="galaxy.datatypes.proteomics:MzData"/>

To stay up to date with Galaxy’s progress, watch our screencasts; visit our community Hub; and follow us on Bluesky, Mastodon, and LinkedIn.

You can always chat with us on Matrix.

Thanks for using Galaxy!

The Galaxy Team