
===========================================================
24.2 Galaxy Release (February 2025)
===========================================================

.. include:: _header.rst

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



**A Wizard-like Export View for Workflow Invocations**. The workflow invocation
export process has been enhanced with a new wizard-like interface, making it
more guided and user-friendly. This interface simplifies complex processes with
many options, providing a step-by-step approach to exporting workflow
invocations.

**Workflow Editor Enhancements: Activity Bar and Undo Stack UI**. The Activity
Bar is now present in the Workflow Editor along side multiple interface
improvements.

**Masthead Revision and Activity Bar Improvements**. The Galaxy masthead has
been revised to achieve consistency and reduce redundancy, aligning its
functionality with the Activity Bar.

**Improved Navigation and Usability of Collection Builders**. To guide users
towards creating collections of the correct type, Galaxy now provides better
navigation via buttons directly on data collection parameters. Users can create
a collection with the required structure for the input, with pre-filtered items
from their current history, also ensuring compatibility with required file
extensions. Additionally, users can upload datasets directly to the collection
builder.

**Enhanced Workflow Invocation View**. The Workflow Invocation View, introduced
in the previous release has been significantly refined to improve the usability
and visualization of workflow runs.

**Display Metrics for Workflow Invocations**. Galaxy now provides a Metrics tab
in the Workflow Invocation View, allowing users to quickly summarize runtime,
memory usage, and core allocation per invocation. This enhancement helps users
better understand the resource usage of their workflows.

**Libraries Modernization: Directory Dataset Picker**. The dataset picker for
user and import directories has been modernized, providing a more intuitive and
user-friendly interface. Users can now easily import files or folders from
their user directory or import directory into a library.

**Live Reporting of Job Console Outputs**. If enabled by the Galaxy
administrators, it will now be possible to view live console output for running
jobs. The job output will be available on the Job Information page where these
logs have always been available for completed jobs.

**ChatGXY - Job Error Wizard**. With this release, we're excited to introduce
ChatGXY — AI assistance built directly into the Galaxy interface. The first
functionality being rolled out is an AI-driven job error diagnoser that
automatically inspects errored jobs and provides actionable insights. Users on
supported servers can access this feature through the Dataset Error interface,
where ChatGXY offers targeted suggestions to help diagnose and resolve job
errors quickly and efficiently.


Please see the `24.2 user release notes <24.2_announce_user.html>`__ for a summary of new user features.

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_24.2 https://github.com/galaxyproject/galaxy.git

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

      $ git fetch origin && git checkout release_24.2 && git pull --ff-only origin release_24.2

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

Upcoming Deprecation Notices
===========================================================

**Deprecation of support for Python 3.8 in Galaxy release 25.0**
  This Galaxy release (24.2) will be the last release that supports Python 3.8.
  We encourage updating to a newer version of Python if possible.

Admin Notes
===========================================================

* Migrating the database to 24.2 may require a short downtime. The 24.2
  database migrations require exclusive access to the `galaxy_user` table.
  Therefore, it is recommended to shut down all Galaxy procesess while
  upgrading the database.
* Database migration `04288b6a5b25 (make dataset uuids unique)` requires
  function `gen_random_uuid()` which was added in PostgreSQL version 13.0.
  Prior to version 13.0, UUID generation functions were available in the
  external modules uuid-ossp and pgcrypto (see `PostgreSQL 13.0 release notes
  <https://www.postgresql.org/docs/release/13.0/>`__). Thus, you need to
  upgrade your database to version 13.0 or newer, or, alternatively, load the
  pgcrypto extension (see `this solution on Stackoverflow
  <https://stackoverflow.com/a/35960732/1382596>`__).  * A user's email address
  is no longer used as the name of their private role;
  instead, the association between a user and their private role is handled
  through a foreign key at the database level. Although a role name is no
  longer required to be unique in the database (automatically generated private
  roles have the generic name "private role"), manually created roles still
  must have a unique name; this prevents from accidentally creating duplicate
  roles.
* The user/role/group association tables in the database have been given
  additional constraints which prevent accidental creation of duplicate or
  incomplete records. In addition to these changes to the database schema, the
  database upgrade includes data migration scripts (executed as part of the
  upgrade) which will automatically fix any inconsistent data in these tables.
  [`#18777 <https://github.com/galaxyproject/galaxy/pull/18777>`__]
* OAuth 2.0 enabled plugin for Dropbox has been added to the user defined file
  sources framework. See `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`__
  for updates to the admin documentation on how to build and configure a
  Dropbox app within Dropbox for a Galaxy instance.
* Support has been added for high-availability setups for the interactive tools proxy.
  [`#18481 <https://github.com/galaxyproject/galaxy/pull/18481>`__]


Configuration Changes
===========================================================


Added
-----

The following configuration options are new

config/galaxy.yml.sample:galaxy
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-  mapping.galaxy.mapping.file_source_listings_expiry_time
-  mapping.galaxy.mapping.file_source_temp_dir
-  mapping.galaxy.mapping.file_source_webdav_use_temp_files
-  mapping.galaxy.mapping.interactivetoolsproxy_map
-  mapping.galaxy.mapping.openai_api_key
-  mapping.galaxy.mapping.openai_model
-  mapping.galaxy.mapping.workflow_scheduling_separate_materialization_iteration


Changed
-------

The following configuration options have been changed

config/user_preferences_extra_conf.yml.sample
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-  preferences.onedata.inputs has changed from

   ::

    {'name': 'onezone_domain', 'label': 'Domain of the Onezone service (e.g. datahub.egi.eu)', 'type': 'text', 'required': False}
    {'name': 'access_token', 'label': 'Your access token, suitable for REST API access in a Oneprovider service', 'type': 'password', 'required': False}
    {'name': 'disable_tls_certificate_validation', 'label': 'Allow connection to Onedata servers that do not present trusted SSL certificates. SHOULD NOT be used unless you really know what you are doing.', 'type': 'boolean', 'required': False, 'value': False}

   to

   ::

    {'name': 'onezone_domain', 'label': 'Domain of the Onezone service (e.g. datahub.egi.eu). The minimal supported Onezone version is 21.02.4.', 'type': 'text', 'required': False}
    {'name': 'access_token', 'label': 'Your access token, suitable for REST API access in a Oneprovider service', 'type': 'password', 'required': False}
    {'name': 'disable_tls_certificate_validation', 'label': 'Allow connection to Onedata servers that do not present trusted SSL certificates. SHOULD NOT be used unless you really know what you are doing.', 'type': 'boolean', 'required': False, 'value': False}



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', 'access_token': "${user.preferences['dropbox|access_token']}"}
    {'type': 'webdav', 'id': 'owncloud1', 'label': 'OwnCloud', 'doc': 'External OwnCloud files (configure access in user preferences)', 'url': "${user.preferences['owncloud|url']}", 'root': "${user.preferences['owncloud|root']}", 'login': "${user.preferences['owncloud|username']}", 'password': "${user.preferences['owncloud|password']}", 'temp_path': '/your/temp/path', 'writable': False}
    {'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}
    {'type': 'http', 'label': 'Custom http filesource', 'id': 'httpcustom', 'url_regex': '^https?://myprotectedsite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'myprotectedsite|username\'] + ":" + user.preferences[\'myprotectedsite|password\'])).decode()}'}, 'doc': 'Only define this if you want custom control over http downloads. You should also define a stock http source (below) or only downloads from this site will be allowed.'}
    {'type': 'http', 'label': 'Stock http filesource', 'id': 'httpstock', 'doc': 'Make sure to define this generic http file source if you have defined any other http file sources, or stock http download capability will be disabled.'}
    {'type': 'drs', 'label': 'Custom DRS filesource', 'id': 'drscustom', 'url_regex': '^drs://mydrssite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'mydrssite|username\'] + ":" + user.preferences[\'mydrssite|password\'])).decode()}'}, 'doc': 'Define this if you want custom control over drs downloads. You should also define a stock drs source (below) or only downloads from this drs server will be allowed.'}
    {'type': 'drs', 'label': 'Stock DRS filesource', 'id': 'drsstock', 'doc': 'Make sure to define this generic drs file source if you have defined any other drs file sources, or stock drs download capability will be disabled.'}
    {'type': 'inveniordm', 'id': 'invenio_sandbox', 'doc': 'This is the Sandbox instance of Invenio. It is used for testing purposes only, content is NOT preserved. DOIs created in this instance are not real and will not resolve.', 'label': 'Invenio RDM Sandbox Repository (TESTING ONLY)', 'url': 'https://inveniordm.web.cern.ch/', 'token': "${user.user_vault.read_secret('preferences/invenio_sandbox/token')}", 'public_name': "${user.preferences['invenio_sandbox|public_name']}", 'writable': True}
    {'type': 'zenodo', 'id': 'zenodo', 'doc': 'Zenodo is a general-purpose open-access repository developed under the European OpenAIRE program and operated by CERN. It allows researchers to deposit data sets, research software, reports, and any other research-related digital artifacts. For each submission, a persistent digital object identifier (DOI) is minted, which makes the stored items easily citeable.', 'label': 'Zenodo', 'url': 'https://zenodo.org', 'token': "${user.user_vault.read_secret('preferences/zenodo/token')}", 'public_name': "${user.preferences['zenodo|public_name']}", 'writable': True}
    {'type': 'zenodo', 'id': 'zenodo_sandbox', 'doc': 'This is the Sandbox instance of Zenodo. It is used for testing purposes only, content is NOT preserved. DOIs created in this instance are not real and will not resolve.', 'label': 'Zenodo Sandbox (TESTING ONLY)', 'url': 'https://sandbox.zenodo.org', 'token': "${user.user_vault.read_secret('preferences/zenodo_sandbox/token')}", 'public_name': "${user.preferences['zenodo_sandbox|public_name']}", 'writable': True}
    {'type': 'onedata', 'id': 'onedata1', 'label': 'Onedata', 'doc': 'Your Onedata files - configure an access token via user preferences', 'accessToken': "${user.preferences['onedata|access_token']}", 'onezoneDomain': "${user.preferences['onedata|onezone_domain']}", 'disableTlsCertificateValidation': "${user.preferences['onedata|disable_tls_certificate_validation']}"}

   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', 'access_token': "${user.preferences['dropbox|access_token']}"}
    {'type': 'webdav', 'id': 'owncloud1', 'label': 'OwnCloud', 'doc': 'External OwnCloud files (configure access in user preferences)', 'url': "${user.preferences['owncloud|url']}", 'root': "${user.preferences['owncloud|root']}", 'login': "${user.preferences['owncloud|username']}", 'password': "${user.preferences['owncloud|password']}", 'temp_path': '/your/temp/path', 'writable': False}
    {'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}
    {'type': 'http', 'label': 'Custom http filesource', 'id': 'httpcustom', 'url_regex': '^https?://myprotectedsite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'myprotectedsite|username\'] + ":" + user.preferences[\'myprotectedsite|password\'])).decode()}'}, 'doc': 'Only define this if you want custom control over http downloads. You should also define a stock http source (below) or only downloads from this site will be allowed.'}
    {'type': 'http', 'label': 'Stock http filesource', 'id': 'httpstock', 'doc': 'Make sure to define this generic http file source if you have defined any other http file sources, or stock http download capability will be disabled.'}
    {'type': 'drs', 'label': 'Custom DRS filesource', 'id': 'drscustom', 'url_regex': '^drs://mydrssite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'mydrssite|username\'] + ":" + user.preferences[\'mydrssite|password\'])).decode()}'}, 'doc': 'Define this if you want custom control over drs downloads. You should also define a stock drs source (below) or only downloads from this drs server will be allowed.'}
    {'type': 'drs', 'label': 'Stock DRS filesource', 'id': 'drsstock', 'doc': 'Make sure to define this generic drs file source if you have defined any other drs file sources, or stock drs download capability will be disabled.'}
    {'type': 'inveniordm', 'id': 'invenio_sandbox', 'doc': 'This is the Sandbox instance of Invenio. It is used for testing purposes only, content is NOT preserved. DOIs created in this instance are not real and will not resolve.', 'label': 'Invenio RDM Sandbox Repository (TESTING ONLY)', 'url': 'https://inveniordm.web.cern.ch/', 'token': "${user.user_vault.read_secret('preferences/invenio_sandbox/token')}", 'public_name': "${user.preferences['invenio_sandbox|public_name']}", 'writable': True}
    {'type': 'zenodo', 'id': 'zenodo', 'doc': 'Zenodo is a general-purpose open-access repository developed under the European OpenAIRE program and operated by CERN. It allows researchers to deposit data sets, research software, reports, and any other research-related digital artifacts. For each submission, a persistent digital object identifier (DOI) is minted, which makes the stored items easily citeable.', 'label': 'Zenodo', 'url': 'https://zenodo.org', 'token': "${user.user_vault.read_secret('preferences/zenodo/token')}", 'public_name': "${user.preferences['zenodo|public_name']}", 'writable': True}
    {'type': 'zenodo', 'id': 'zenodo_sandbox', 'doc': 'This is the Sandbox instance of Zenodo. It is used for testing purposes only, content is NOT preserved. DOIs created in this instance are not real and will not resolve.', 'label': 'Zenodo Sandbox (TESTING ONLY)', 'url': 'https://sandbox.zenodo.org', 'token': "${user.user_vault.read_secret('preferences/zenodo_sandbox/token')}", 'public_name': "${user.preferences['zenodo_sandbox|public_name']}", 'writable': True}
    {'type': 'onedata', 'id': 'onedata1', 'label': 'Onedata', 'doc': 'Your Onedata files - configure an access token via user preferences', 'access_token': "${user.preferences['onedata|access_token']}", 'onezone_domain': "${user.preferences['onedata|onezone_domain']}", 'disable_tls_certificate_validation': "${user.preferences['onedata|disable_tls_certificate_validation']}"}



config/galaxy.yml.sample:galaxy
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-  mapping.galaxy.mapping.conda_auto_init.desc has changed from

   ::

    Set to true to instruct Galaxy to install Conda from the web automatically
    if it cannot find a local copy and conda_exec is not configured.

   to

   ::

    Set to true to instruct Galaxy to install Conda from the web automatically
    if it cannot find a local copy and conda_exec is not configured. The default is
    true if running Galaxy from source, and false if running from installed packages.


-  mapping.galaxy.mapping.geographical_server_location_code.desc has changed from

   ::

    The estimated geographical location of the server hosting your galaxy instance given as an ISO 3166 code.
    This is used to make carbon emissions estimates more accurate as the location effects the
    carbon intensity values used in the estimate calculation. This defaults to "GLOBAL" if not set or the
    `geographical_server_location_code` value is invalid or unsupported. To see a full list of supported locations,
    visit https://galaxyproject.org/admin/carbon_emissions

   to

   ::

    The estimated geographical location of the server hosting your galaxy instance given as an ISO 3166 code.
    This is used to make carbon emissions estimates more accurate as the location effects the
    carbon intensity values used in the estimate calculation. This defaults to "GLOBAL" if not set or the
    `geographical_server_location_code` value is invalid or unsupported. To see a full list of supported locations,
    visit https://docs.galaxyproject.org/en/master/admin/carbon_emissions.html


-  mapping.galaxy.mapping.interactivetools_map.desc has changed from

   ::

    Map for interactivetool proxy.

   to

   ::

    Map for the interactivetool proxy. Mappings are stored in a SQLite database file
    located on this path. As an alternative, you may also store them in any other RDBMS
    supported by SQLAlchemy using the option ``interactivetoolsproxy_map``, which
    overrides this one.


-  mapping.galaxy.mapping.object_store_cache_size.desc has changed from

   ::

    Default cache size for caching object stores if cache not configured for
    that object store entry.

   to

   ::

    Default cache size, in GB, for caching object stores if the cache is not
    configured for that object store entry.


Removed
-------

The following configuration options have been completely removed

config/galaxy.yml.sample:galaxy
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-  mapping.galaxy.mapping.conda_auto_init


Developer Notes
===========================================================

* More concise, readable tool execution testing: infrastructure and some examples. [`#18977 <https://github.com/galaxyproject/galaxy/pull/18977>`__]
* More examples of new data access tests. [`#18312 <https://github.com/galaxyproject/galaxy/pull/18312>`__]
* Poetry replaced: Galaxy's Python dependency management is now handled with uv. [`#19075 <https://github.com/galaxyproject/galaxy/pull/19075>`__]
* Upgrades to openapi-typescript cause some breaking changes. See `#18532 <https://github.com/galaxyproject/galaxy/pull/18532>`__ for more details.


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

.. include:: 24.2.rst
   :start-after: announce_start

Release Team
===========================================================

Release manager:  `John Davis <https://github.com/jdavcs>`__, `Ahmed Awan <https://github.com/ahmedhamidawan>`__

Release testing:

* `Patrik Smeds <https://github.com/Smeds>`__
* `Junhao Qiu <https://github.com/qchiujunhao>`__
* `Mina Hojat Ansari <https://github.com/Minamehr>`__
* `John Chilton <https://github.com/jmchilton>`__
* `Jennifer Hillman-Jackson <https://github.com/jennaj>`__
* `Aysam Guerler <https://github.com/guerler>`__
* `Srividya Ramakrishnan <https://github.com/Srividya22>`__

A special thank you goes to everyone who helped test the new release after its deployment on usegalaxy.org.

----

.. include:: _thanks.rst
