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September 2019 Galaxy Release (v 19.09)

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Highlights

Interactive Tools

A new type of Galaxy tool has been implemented that allows interactive experiences like Galaxy Interactive Environments (via a proxy and Docker containers) but using plugins defined with Galaxy’s XML tool syntax. Dan Blankenberg’s slides on these new features from Galaxy Community Conference 2019 can be found here. More information can be found in the original pull request, including interactive tool versions of all of Galaxy’s bundled interactive environments Pull Request 7494.

Workflow Invocation Reports

Workflows may now define Markdown templates with Galaxy-specific embedded syntax extensions that can tie together workflow inputs, outputs, jobs, and metadata into rich reports. More information on the motivation for these reports can be found in these slides, implementation details and GUI enhancements are described in the original pull request (#8030), and details on the final syntax selected for embedded Galaxy objects can be found in the pull request that was ultimately merged (#8543).

New Toolshed Client Interface

The march toward replacing templated backend-generated HTML with modern, reactive components continued in Galaxy 19.09. Galaxy’s tool panel, job properties tables, job management controls, and “Pages” infrastructure were all replaced with VueJS components (with huge help from @scrathat and @inkuzmin). Most notably, Galaxy’s interface to the Tool Shed was also rewritten in VueJS and is now completely API driven. This project drove numerous enhancements to the Tool Shed API, including vastly improved search functionality. This interface has been completely re-imagined and feels much more interactive.

Also check out the 19.09 user release notes.

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_19.09 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_19.09 && git pull --ff-only origin release_19.09

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

Tool configuration file handling changes

Shed tool configuration file

There have been a few changes to the way that Galaxy loads tool panel configuration files (e.g. tool_conf.xml and shed_tool_conf.xml) that deployers should be aware of before upgrading.

A new configuration option named shed_tool_config_file has been added, with a default value of config/shed_tool_conf.xml, and that path has been removed from the default value of the tool_config_file option. This new option makes it possible for Galaxy to create the shed tool configuration file (e.g. shed_tool_conf.xml) file on demand and moves us one step closer to a Galaxy installation that does not need to be run from the root of its source directory.

If you make no changes to your configuration, you should not encounter any problems. However, if you are using a non-default path to your primary shed tool config file, you should modify these options to remove the path of your primary shed_tool_conf.xml from tool_config_file and set it in shed_tool_config_file. Although Galaxy will continue to operate properly if you do not make this change, failure to do so will result in a second shed tool panel config file being created and loaded at startup time.

Although an unusual configuration, if you have multiple shed tool config files, you can still load them in tool_config_file, just be sure that one of them is set in shed_tool_config_file.

Note that Galaxy will fail to start if any of the files specified in tool_conf_file cannot be read at startup, whereas it will only fail to start if the file specified in shed_tool_config_file cannot be created (if it does not already exist).

Migrated tools configuration file

Galaxy contains a (now unused) system for automatically installing tools from the Tool Shed that had been migrated out of the Galaxy source code after the creation of the Tool Shed. Older deployments that used this system may have tools in the migrated tools config file, config/migrated_tools_conf.xml.sample (by default). As of this release, an empty migrated_tools_conf.xml file is not created by default for new installations, but will still be read if it is found at the default path. The path can be changed with the migrated_tools_config option, and you can force Galaxy to fail startup if the file is missing by adding it to the tool_config_file option.

Configuration file path defaults

Deprecated paths will no longer be searched The default location for Galaxy’s configuration files has been in the config/ directory for many years, prior to which the default was the root of the Galaxy directory. As of this release, Galaxy will no longer look in the current directory for configuration files, so you will need to specify the path to galaxy.yml e.g. with uwsgi --yaml /path/to/galaxy.yml, GALAXY_CONFIG_FILE=/path/to/galaxy.yml run.sh, or similar means, if it is not in the default location.

Default paths to additional configuration files As of this release, all other configuration files (e.g. datatypes_conf.xml, job_conf.xml) are searched for in the same directory as galaxy.yml. Prior to this release, the default was in the config/ directory of the current working directory at startup (which has always been, and for the time being continues to be, the root of the Galaxy source). This means that you do not need to individually configure the paths to these files in galaxy.yml if you are storing them in non-default locations.

MySQL Support Drop

The MySQL database server is no longer officially supported and all deployers are urged to use PostgreSQL.

Deprecation Notice

API

The following Galaxy API endpoints (related to the Toolshed) are considered deprecated and staged for removal in the next release:

  • api/toolshed/ { category | repository | search | show | status | tool_json }

  • api/toolshed_repositories/ { check_for_updates | exported_workflows | get_latest_installable_revision | import_workflow | import_workflows | install | repair_repository_revision | shed_category | shed_repository | shed_search | status }

Python

TL;DR Galaxy can be deployed on both Python 2 and 3, with Python 3 expected to be the increasingly encouraged way of deployment.

Python 2 will not be maintained past 2020 which means Galaxy 19.09 is the last release that officially supports Python 2.

Over the past years the Galaxy team has made a substantial effort, spearheaded by @nsoranzo and @mvdbeek, to make Galaxy compatible with Python 3. Thanks to this endeavor the Galaxy Test server has been running on Python 3 since April of this year and Galaxy itself now fully supports Python 3.

Galaxy Tools, that properly declare their Python dependency (using e.g. <requirement type="package" version="2.7">python</requirement>), will continue to work as expected with Python 2 being provided by Conda. However tools that naively rely on the implicit presence of Python 2 on the PATH may fail on Python3 deployments. Another corner case are tools that use Python2-specific Cheetah templating syntax in their XML. We have implemented various mitigation approaches on the Galaxy side, but some old tools using this syntax will not function correctly.

In our testing these problems should affect only a very limited number of tools and the vast majority should work on Python 3 without a change.

GenomeSpace

The GenomeSpace project has ended on November 15, 2019 due to expiration of its NHGRI funding. Therefore the GenomeSpace Importer and Exporter Galaxy tools are hereby deprecated and will be removed in 20.01.

Release Notes

Enhancements

Fixes

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