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September 2021 Galaxy Release (v 21.09)

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Highlights

Tool Panel Views

With many thousands of Tools available on public Galaxy instances it is often difficult to organize and find Tools in the Tool Panel. To address this problem we are introducing Tool Panel Views. Administrators can configure an arbitrary number of Tool Panel Views. These views can be constructed automatically for Tools annotated with EDAM terms, or they can be constructed manually by referring to existing Sections, Tools or Workflows. Users can then select the Tool Panel View most appropriate to their current activity. The default Tool Panel View corresponds uses the sections as they are traditionally configured. It is also possible to configure the default Tool Panel View using the domain name of the server, so “flavors” of Galaxy can be created based on the URL that users use to interact with a server, while behind the scenes these flavors are served by the same Galaxy process. For more details see the 21.09 user release notes and PullRequest12327. (Pull Request 12327, Pull Request 12677, Pull Request 12328, Pull Request 12379).

Enhancements for Working with Remote Data and Distributed Computing Resources

Many fixes and enhancements were made to improve how Galaxy can import and write to remote data locations using the configured file source plugins. In addition to the History Export functionality, which can write to remote locations we have added an Export datasets Tool for exporting individual Datasets and Dataset collections to configured remote locations. The Tool will automatically maintain the name and structure of Datasets and Dataset Collections. We have added the possibility to import entire folders of remote data and made the data selection dialog more intuitive. We also added numerous improvements and fixes to the extended metadata collection strategy and Pulsar, so that many more Tools are able to run in Pulsar and write data back to storage without passing through Galaxy first. (Pull Request 12785, Pull Request 11613, Pull Request 12250, Pull Request 12372, Pull Request 12760, Pull Request 12267, Pull Request 11949, Pull Request 12310, Pull Request 12388, Pull Request 12641).

Migration to FastAPI and Extended Documentation of API Routes

We have modernized and migrated many more API routes to FastAPI and have extended the documentation and validation of these routes. (Pull Request 11315, Pull Request 11827, Pull Request 11983, Pull Request 12131, Pull Request 12337, Pull Request 12195, Pull Request 12370, Pull Request 12391, Pull Request 12417, Pull Request 12505).

Migration to SQLAlchemy 1.4 and Declarative Mapping

Galaxy is now using SQLAlchemy version 1.4, which is a prerequisite for asynchronously interacting with the database. We also modernized the way our database models are defined to the more commonly used declarative mapping approach, which is more concise and better documented. (Pull Request 12042, Pull Request 12045, Pull Request 12064, Pull Request 12438, Pull Request 12060, Pull Request 12424, Pull Request 12461).

Modernization of Tool Form Interface

The Tool Form interface has been almost completed migrated from Backbone to Vue. This improves the reactivity of parameter validation and enables the migration of Tool parameters to Vue, which will also allows us to add many more types of Tool parameters. We further migrated the Tool Form variant for the Workflow Editor, the Workflow Run Form and the Show Dataset Parameter page to Vue. (Pull Request 12300, Pull Request 12031, Pull Request 12227, Pull Request 12296, Pull Request 12323, Pull Request 12329, Pull Request 12374, Pull Request 12432, Pull Request 12702, Pull Request 12261).

New User Welcome Page

We have added a page that new users will be directed to after creating a new Galaxy account. (Pull Request 11085, Pull Request 12639)

Also check out the 21.09 user release notes

Deprecation Notices

Galaxy Interactive Environments (GIEs) are not visible anymore in the User Interface and will be completely removed in the next Galaxy release (22.01). All GIEs have been ported to Interactive Tools, which are much easier to develop, run and configure.

Upcoming Deprecation Notices

We have postponed the following deprecations to the next Galaxy release in order to prepare a smoother experience for our users and administrators.

Deprecation of support for Python 3.6 in Galaxy release 22.01

This Galaxy release (21.09) will be the last release that supports Python 3.6 or newer. We encourage updating to a newer Python if possible.

Deprecation of uwsgi and paste

This Galaxy release (21.09) will be the last release that supports the WSGI standard, and with it uwsgi and paste. From release 22.01 Galaxy will be an ASGI application. We will update documentation and playbooks during the upcoming development cycle to enable a smooth transition.

Configuration Changes

Added

The following configuration options are new

config/galaxy.yml.sample:galaxy

  • biotools_content_directory

  • biotools_service_cache_data_dir

  • biotools_service_cache_lock_dir

  • biotools_service_cache_type

  • biotools_use_api

  • container_resolvers

  • default_panel_view

  • edam_panel_views

  • edam_toolbox_ontology_path

  • enable_account_interface

  • job_handler_monitor_sleep

  • job_runner_monitor_sleep

  • mailing_join_body

  • mailing_join_subject

  • mailing_lists_url

  • panel_views

  • panel_views_dir

  • sentry_event_level

Changed

The following configuration options have been changed

config/error_report.yml.sample

  • has changed from

{'type': 'email', 'verbose': True, 'user_submission': True}
{'type': 'sentry', 'user_submission': False}

to

{'type': 'email', 'verbose': True, 'user_submission': True}

config/file_sources_conf.yml.sample

  • has changed from

{'type': 'dropbox', 'id': 'dropbox1', 'label': 'Dropbox files (configure access in user preferences)', 'doc': 'Your Dropbox files - configure an access token via the user preferences', 'accessToken': "${user.preferences['dropbox|access_token']}"}
{'type': 'webdav', 'id': 'owncloud1', 'label': 'OwnCloud', 'doc': 'External OwnCloud files (configure access in user preferences)', 'url': "${user.preferences['owncloud|url']}", 'root': "${user.preferences['owncloud|root']}", 'login': "${user.preferences['owncloud|username']}", 'password': "${user.preferences['owncloud|password']}"}
{'type': 'posix', 'id': 'posix1', 'label': 'Posix', 'doc': 'Files from local path', 'root': '/some/path/'}
{'type': 's3fs', 'label': 'My MinIO storage', 'endpoint_url': 'https://minio.usegalaxy.eu', 'id': 'galaxy-minio-storage', 'doc': 'Galaxy MinIO S3 storage', 'anon': False, 'secret': 'UHAJ6asd6asdhasd', 'key': 'MCJU76agdt98GGFAROIP7'}
{'type': 's3fs', 'label': 'CMIP6 GCMs downscaled using WRF', 'id': 'wrf-cmip6-noversioning', 'doc': 'High-resolution historical and future climate simulations from 1980-2100', 'bucket': 'wrf-cmip6-noversioning', 'anon': True}

to

{'type': 'dropbox', 'id': 'dropbox1', 'label': 'Dropbox files (configure access in user preferences)', 'doc': 'Your Dropbox files - configure an access token via the user preferences', 'accessToken': "${user.preferences['dropbox|access_token']}"}
{'type': 'webdav', 'id': 'owncloud1', 'label': 'OwnCloud', 'doc': 'External OwnCloud files (configure access in user preferences)', 'url': "${user.preferences['owncloud|url']}", 'root': "${user.preferences['owncloud|root']}", 'login': "${user.preferences['owncloud|username']}", 'password': "${user.preferences['owncloud|password']}"}
{'type': 'posix', 'root': '/data/5/galaxy_import/galaxy_user_data/covid-19/data/sequences/', 'id': 'covid19-raw-sequences', 'label': 'COVID-19 FASTQ', 'doc': 'COVID-19 RAW sequences in FASTQ format'}
{'type': 'posix', 'root': '/data/db/databases/pdb/pdb/', 'id': 'pdb-gzip', 'doc': 'Protein Data Bank (PDB)', 'label': 'PDB'}
{'type': 'ftp', 'id': 'ebi-ftp', 'label': 'EBI FTP server', 'doc': 'European Bioinformatic Institute FTP server', 'host': 'ftp.ebi.ac.uk', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
{'type': 'ftp', 'id': 'ncbi-ftp', 'label': 'NCBI FTP server', 'doc': 'NCBI FTP server', 'host': 'ftp.ncbi.nlm.nih.gov', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
{'type': 'ftp', 'id': 'ensembl-ftp', 'label': 'ENSEMBL FTP server', 'doc': 'ENSEMBL FTP server', 'host': 'ftp.ensemblgenomes.org/vol1/pub/', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
{'type': 'ssh', 'id': 'writeable-ssh-dir', 'requires_roles': 'writeable-galaxy-role', 'writable': True, 'label': 'Push your files to me', 'doc': 'This is an example of a writeable SSH dir', 'host': 'coolhost', 'user': 'user', 'passwd': 'passwd', 'timeout': 10, 'path': '/home/cooluser/', 'config_path': '', 'port': 2222}
{'type': 's3fs', 'label': 'My MinIO storage', 'endpoint_url': 'https://minio.usegalaxy.eu', 'id': 'galaxy-minio-storage', 'doc': 'Galaxy MinIO S3 storage', 'anon': False, 'secret': 'UHAJ6asd6asdhasd', 'key': 'MCJU76agdt98GGFAROIP7'}
{'type': 's3fs', 'label': 'Genome Ark', 'id': 'genomeark', 'doc': 'Access to Genome Ark open data on AWS.', 'bucket': 'genomeark', 'anon': True}
{'type': 's3fs', 'label': '1000 Genomes', 'id': '1000genomes', 'doc': 'Access to the 1000 Genomes Project with human genetic variation, including SNPs, structural variants, and their haplotype context.', 'bucket': '1000genomes', 'anon': True}
{'type': 's3fs', 'label': 'The Cancer Genome Atlas', 'id': 'tcga-2-open', 'doc': 'Access to the Cancer Genome Atlas (TCGA)', 'bucket': 'tcga-2-open', 'anon': True}
{'type': 's3fs', 'label': 'COVID-19 Data Lake', 'id': 'covid19-lake', 'doc': 'A centralized repository of up-to-date and curated datasets on or related to the spread and characteristics of the novel corona virus (SARS-CoV-2) and its associated illness, COVID-19', 'bucket': 'covid19-lake', 'anon': True}
{'type': 's3fs', 'label': 'Encyclopedia of DNA Elements (ENCODE)', 'id': 'encode-public', 'doc': 'The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)', 'bucket': 'encode-public', 'anon': True}
{'type': 's3fs', 'label': 'Sentinel-3', 'id': 'meeo-s3-nrt', 'doc': 'European Commission’s Copernicus Earth Observation Programme. Sentinel-3 is a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s3/NRT/', 'anon': True}
{'type': 's3fs', 'label': 'Sentinel-5P Level 2', 'id': 'meeo-s5p-nrti', 'doc': 'Observations from the Sentinel-5 Precursor satellite of the Copernicus Earth Observation Programme. It contains a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s5p/RPRO/', 'anon': True}
{'type': 's3fs', 'label': 'Coupled Model Intercomparison Project 6', 'id': 'esgf-world', 'doc': 'The sixth phase of global coupled ocean-atmosphere general circulation model ensemble', 'bucket': 'esgf-world', 'anon': True}
{'type': 's3fs', 'label': 'CMIP6 GCMs downscaled using WRF', 'id': 'wrf-cmip6-noversioning', 'doc': 'High-resolution historical and future climate simulations from 1980-2100', 'bucket': 'wrf-cmip6-noversioning', 'anon': True}
{'type': 's3fs', 'label': 'NOAA Global Forecast System (GFS)', 'id': 'noaa-gfs-bdp-pds', 'doc': 'The Global Forecast System (GFS) is a weather forecast model produced by the National Centers for Environmental Prediction (NCEP).', 'bucket': 'noaa-gfs-bdp-pds', 'anon': True}
{'type': 's3fs', 'label': 'NOAA Unified Forecast System Subseasonal to Seasonal Prototype 5', 'id': 'noaa-ufs-prototype5-pds', 'doc': 'The Unified Forecast System Subseasonal to Seasonal prototype 5 (UFS S2Sp5) dataset is reforecast data from the UFS atmosphere-ocean.', 'bucket': 'noaa-ufs-prototype5-pds', 'anon': True}
{'type': 's3fs', 'label': 'Copernicus Digital Elevation Model (DEM)', 'id': 'copernicus-dem-30m', 'doc': 'The Copernicus DEM is a Digital Surface Model (DSM) which represents the surface of the Earth including buildings, infrastructure and vegetation.', 'bucket': 'copernicus-dem-30m', 'anon': True}

config/galaxy.yml.sample:galaxy

  • dependency_resolvers description has changed from

    Rather than specifying a dependency_resolvers_config_file, the definition of the
resolvers to enable can be embedded into Galaxy's config with this option.
This has no effect if a dependency_resolvers_config_file is used.

    to

    Rather than specifying a dependency_resolvers_config_file, the definition of the
resolvers to enable can be embedded into Galaxy's config with this option.
This has no effect if a dependency_resolvers_config_file is used.

The syntax, available resolvers, and documentation of their options is explained in detail in the
documentation:

https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html

  • dependency_resolvers_config_file description has changed from

    The dependency resolvers config file specifies an ordering and options for how
Galaxy resolves tool dependencies (requirement tags in Tool XML). The default
ordering is to the use the Tool Shed for tools installed that way, use local
Galaxy packages, and then use Conda if available.
See https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst
for more information on these options.

    to

    Specifies the path to the standalone dependency resolvers configuration file. This
configuration can now be specified directly in the Galaxy configuration, see the
description of the 'dependency_resolvers' option for details.

  • ftp_upload_dir description has changed from

    Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
configure an FTP server (we've used ProFTPd since it can use Galaxy's
database for authentication) and set the following two options.
This should point to a directory containing subdirectories matching users'
identifier (defaults to e-mail), where Galaxy will look for files.

    to

    This should point to a directory containing subdirectories matching users'
identifier (defaults to e-mail), where Galaxy will look for files.

  • ftp_upload_site description has changed from

    This should be the hostname of your FTP server, which will be provided to
users in the help text.

    to

    Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
configure an FTP server (we've used ProFTPd since it can use Galaxy's
database for authentication) and set the following two options.
This will be provided to users in the help text as 'log in to the FTP
server at '. Thus, it should be the hostname of your FTP server.

  • mailing_join_addr description has changed from

    On the user registration form, users may choose to join a mailing list. This
is the address used to subscribe to the list. Uncomment and leave empty if you
want to remove this option from the user registration form.

Example value 'galaxy-announce-join@bx.psu.edu'

    to

    On the user registration form, users may choose to join a mailing list. This
is the address used to subscribe to the list. Uncomment and leave empty if you
want to remove this option from the user registration form.

Example value 'galaxy-announce-join@lists.galaxyproject.org'

  • toolbox_filter_base_modules default has changed from

    galaxy.tools.filters,galaxy.tools.toolbox.filters

    to

    galaxy.tools.filters,galaxy.tools.toolbox.filters,galaxy.tool_util.toolbox.filters

Removed

The following configuration options have been completely removed

config/galaxy.yml.sample:galaxy

  • beta_edam_toolbox_ontology_path

  • containers_resolvers_config_file

  • enable_beta_edam_toolbox

  • enable_job_recovery

  • sentry_sloreq_threshold

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_21.09 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_21.09 && git pull --ff-only origin release_21.09

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

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