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September 2021 Galaxy Release (v 21.09)¶

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 anExport 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
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¶
- New User Welcome page (thanks to @astrovsky01). Pull Request 11085
- GPU enabled jupyter notebook for machine learning powered by Jupyter lab and Tensorflow (thanks to @anuprulez). Pull Request 11484
- NCBI Datasets data source tool Pull Request 11738
- Feature/6965/change datatype and dbkey (thanks to @assuntad23). Pull Request 11799
- Add “View Details” button for collections Pull Request 12261
- Vuefy and improve granularity for tool HTML sanitization Pull Request 12283
- Implement tool panel views. Pull Request 12327
- Implement news webhook to handle release announcements (thanks to @hexylena). Pull Request 12396
- Various fixes and enhancements for metadata_strategy: extended Pull Request 12785
- Convert/standardize to fstrings across lib Pull Request 11338
- Added documentation for FASTQ datatypes and implemented quality check (thanks to @bernt-matthias). Pull Request 11931
- Make dataset preview for h5mlm datatype (thanks to @qiagu). Pull Request 11935
- Add datatypes for Structural Materials Hexrd application (thanks to @jj-umn). Pull Request 11957
- Adding new subclass types (thanks to @maikenp). Pull Request 12097
- Converters: use target datatype (thanks to @bernt-matthias). Pull Request 12185
- Add bref3 datatype (thanks to @gallardoalba). Pull Request 12199
- Converters: add missing tests and add linting to converter tests (thanks to @bernt-matthias). Pull Request 12202
- Converters: Unify converters to tabix and bgzip (thanks to @bernt-matthias). Pull Request 12213
- Unify dcd, trr, xtc datatype converters (thanks to @bernt-matthias). Pull Request 12224
- Unify bcf datatype converters (thanks to @bernt-matthias). Pull Request 12225
- Add “ExpressionSet RData object” Datatype (thanks to @mtekman). Pull Request 12336
- Parse sam metadata from sam files (thanks to @bernt-matthias). Pull Request 12392
- Add ONNX datatype (thanks to @anuprulez). Pull Request 12429
- Add support for RDS files and improvements for RData (thanks to @bernt-matthias). Pull Request 12712
- Changes to Collection Operation Help sections and parameter names Pull Request 11068
- Update bam.iobio interactive tool wrapper (thanks to @luke-c-sargent). Pull Request 11537
- Add tool for exporting individual files to galaxy file source plugins. Pull Request 11613
- Update AskOmics interactive tool to 4.3.1 (thanks to @abretaud). Pull Request 12159
- Add
<creator>
to the tool schema template, use live links in xsd Pull Request 12242 - Systematic handling of remotely required tool files. Pull Request 12250
- Allow bio.tools mappings for legacy tools. Pull Request 12289
- Allow skipping sanitization of / char in export_remote tool Pull Request 12372
- Lock location file before adding values Pull Request 12446
- Improve error handling in DirectoryUriToolParameter validation (thanks to @davelopez). Pull Request 12760
- Beta history selenium updates and assorted bug fixes Pull Request 12351
- Document how to run a local UI client against a remote Galaxy server (thanks to @OlegZharkov). Pull Request 12356
- Charts downloads fixes and enhancements. Pull Request 12726
- SGE DRMAA example for queue, RAM and CPUs request (thanks to @pcm32). Pull Request 12059
- Allow specifying useful classes of tools for mapping in job conf YAML/XML Pull Request 12258
- Fix galaxy.json dynamic file collection in Pulsar. Pull Request 12267
- Default
k8s_unschedulable_walltime_limit
toNone
and allow for unlimited queue wait time (thanks to @nuwang). Pull Request 12317 - Support setting per-job-environment container resolvers using the container_resolvers key in the environment config Pull Request 12350
- Add config options for controlling handler and runner monitor thread sleep. Pull Request 12473
- Make conda_auto_init option overrridable (thanks to @rhpvorderman). Pull Request 12200
- Support setting the container resolvers configuration directly in the Galaxy app config Pull Request 12344
- Improve k8s docker image (thanks to @nuwang). Pull Request 12373
- Fix sorting on disk_usage column in admin panel (thanks to @cat-bro). Pull Request 12469
- Make the subject and body of the mailing list join message configurable Pull Request 12484
- Don’t change panel view after installing repositories, clean up provider Pull Request 12677
- Test configuration for running Selenium tests against beta history panel. Pull Request 10965
- Add
negate
attribute to validators and tests (thanks to @bernt-matthias). Pull Request 11043 - Allow element_identifiers or a manually specified name for datasets in build list tool (thanks to @bernt-matthias). Pull Request 11309
- Prepare FastAPI route for quotas (thanks to @davelopez). Pull Request 11315
- Create central pydantic models (thanks to @davelopez). Pull Request 11827
- Use python:3.7-slim container instead of ubuntu (thanks to @rhpvorderman). Pull Request 11855
- Add more examples for the file source plugins (thanks to @bgruening). Pull Request 11949
- Migrate Libraries API (top level) to FastAPI (thanks to @davelopez). Pull Request 11983
- Upgraded to v0.9.0 of irods client that supports parallel put/get (thanks to @kxk302). Pull Request 11984
- Improve handling of tags for collection manipulation tools (thanks to @simonbray). Pull Request 11992
- Initial setup for migrating to declarative mapping Pull Request 12042
- Migrate model to declarative mapping Pull Request 12045
- Unify nested collection attribute or instance access Pull Request 12056
- Increase API tests coverage for Data Library GET permissions (thanks to @davelopez). Pull Request 12057
- Tweak PR template to be a bit more flexible and lightweight. Pull Request 12063
- Declarative mappings + tests for all models Pull Request 12064
- Enable pytest class-based tests Pull Request 12072
- Rework variable name to clarify this is a wsgi application. Pull Request 12090
- Upgraded irods client to v1.0.0 (thanks to @kxk302). Pull Request 12101
- Add configuration option to hide user account management interfaces Pull Request 12103
- Fix up some typing redundancy. Pull Request 12108
- Rename dataset_collections_service to dataset_collection_manager. Pull Request 12110
- Allow multiple input datasets in jupyter interactive tool Pull Request 12113
- Change GIE label to interactive-tools Pull Request 12114
- Add FastAPI routes for Library Folders (thanks to @davelopez). Pull Request 12131
- Change icon for “Share or Publish” in new history panel (thanks to @nsoranzo). Pull Request 12143
- Cleanup use of refresh/undo/redo/sync icons (thanks to @nsoranzo). Pull Request 12145
- Unify how the GalaxyInteractorApi handles JSON requests (thanks to @davelopez). Pull Request 12152
- Hide masthead help resources if resource urls are unavailable Pull Request 12198
- Cancel in progress CI on same branch, cache yarn cache Pull Request 12211
- Show target datatype in datatype conversion (thanks to @bernt-matthias). Pull Request 12230
- Add a note to get Python extension and set interpreter (thanks to @eancelet). Pull Request 12234
- Lint for whitespace in tool XML (thanks to @neoformit). Pull Request 12246
- Use relative path in recursive
discover_datasets
tag Pull Request 12254 - Deprecate data manager version (thanks to @bernt-matthias). Pull Request 12255
- Add linting for tool parameter validators (thanks to @bernt-matthias). Pull Request 12262
- Create a bug-report issue template Pull Request 12265
- Enhance page functionalities in data-library folder (thanks to @OlegZharkov). Pull Request 12270
- Parse edam operation and topic data from bio.tools if available. Pull Request 12291
- Refactor base toolbox code de-coupled from app & config into tool_util. Pull Request 12292
- Vueify Dataset Error Details Page and Form Pull Request 12300
- Implement folder selection in file source upload modal (thanks to @OlegZharkov). Pull Request 12310
- Allow HTML in DatasetStorage view (thanks to @bgruening). Pull Request 12312
- Document the delta attribute of has_size assert in xml schema (thanks to @bernt-matthias). Pull Request 12314
- Accept from_tool_provided_metadata as means to specify the format for discovered datasets in tool linter (thanks to @bernt-matthias). Pull Request 12319
- Add Import Collection Button to Collections embedded in Pages Pull Request 12324
- Allow various configuration parameters to be set per host. Pull Request 12328
- Migrate group_roles endpoints to FastAPI (thanks to @ZimmerA). Pull Request 12337
- Restore Upload dialog in global Galaxy object Pull Request 12339
- Move page export button to title Pull Request 12340
- API test case to ensure model attributes get escaped during tool evaluation Pull Request 12357
- Provide more context in EDAM Tool Panel Pull Request 12365
- Mention collection name and element identifier when test comparison fails (thanks to @bernt-matthias). Pull Request 12376
- Extend per_host configurations to include static directories and files. Pull Request 12379
- Display Tabular datasets as sortable tables, and PDF and HTML in embedded frames in Pages Pull Request 12387
- Create directories when needed for the pyfilesystem export plugins (thanks to @bgruening). Pull Request 12388
- Add Instructions for debugging Galaxy connected to a Slurm cluster in VSCode (thanks to @kxk302). Pull Request 12403
- Don’t allow beta history panel Selenium tests to fail. Pull Request 12409
- Selenium test for EDAM tool panel views. Pull Request 12422
- Spanish Translations for remaining untranslated UI components (thanks to @hexylena). Pull Request 12427
- Improvements to Selenium testing Pull Request 12433
- Update refgenconf (refgenie) to 0.12.0. Requires version 0.4 of confi… Pull Request 12435
- Set default constructor for SA models Pull Request 12438
- FastAPI: add middleware to deal with file downloads (thanks to @davelopez). Pull Request 12441
- Add options to override the history name and reuse histories in the tool test script Pull Request 12466
- Let invalid tool profile trigger linter error (thanks to @bernt-matthias). Pull Request 12501
- Release note draft Pull Request 12567
- Use new sentry-sdk and adapt usage pattern Pull Request 12584
- Add client-side validation to tag editor widget Pull Request 12594
- Refgenie fixes for incompatible configurations Pull Request 12617
- Update conditional psycopg2-binary dependency Pull Request 12633
- Adjust appearance of new user welcome page Pull Request 12639
- Fix ambiguity in remote file upload (thanks to @OlegZharkov). Pull Request 12641
- Set wait instead of not-allowed cursor to indicate tool form loading Pull Request 12681
- Fix missing history or hid for History Dataset Associations Pull Request 12721
- 21.09 Release notes for Users (thanks to @hexylena). Pull Request 12734
- Raise Bad Request when bootstrap admins (master key) try to run jobs/tools (thanks to @davelopez). Pull Request 12793
- Add error state to dataset provider, show error in dataset details page Pull Request 12798
- If datatype is unknown display warning when trying to connect nodes Pull Request 12807
- Refactor Sharing (thanks to @OlegZharkov). Pull Request 11701
- Migrate to SQLAlchemy 1.4 Pull Request 11737
- Vueify Workflow Editor wrappers Pull Request 11898
- Add double quotes to cp for from_work_dir (thanks to @bernt-matthias). Pull Request 11960
- Prettier version update to new release Pull Request 12027
- Vueify Tool Form Wrapper Pull Request 12031
- Normalize Vue mounts in analysis, admin endpoints Pull Request 12040
- Set cache_ok flag for SQLAlchemy custom types Pull Request 12060
- Update SQLAlchemy to 1.4.17 Pull Request 12089
- Update dependency resolver docs and drop sample XML file in favor of direct configuration under the dependency_resolvers key of galaxy.yml Pull Request 12105
- Update SQLAlchemy to 1.4.18 Pull Request 12132
- Refactoring: Remove ExportsHistoryMixin and ImportsHistoryMixin (thanks to @davelopez). Pull Request 12146
- Remove unused legacy controller things Pull Request 12172
- Update SQLAlchmey to 1.4.19 Pull Request 12188
- Refactor Histories API controller (thanks to @davelopez). Pull Request 12195
- Unify molecules datatype converters (thanks to @bernt-matthias). Pull Request 12214
- Vueify Workflow Run form Pull Request 12227
- Update SQLAlchmey to 1.4.20 Pull Request 12229
- Refactor History contents API (thanks to @davelopez). Pull Request 12231
- Improve GitHubSearch class (thanks to @nsoranzo). Pull Request 12276
- Some refactoring of interactive tool handling in k8s (thanks to @nuwang). Pull Request 12285
- Replace form-view imports in Visualizations with Vue component layer Pull Request 12296
- Fix histories content filtering by type (thanks to @davelopez). Pull Request 12303
- Vueify Dataset Edit Attributes Pull Request 12323
- Vueify Generic Form Wrapper Pull Request 12329
- Refactor k8s IT checks to make logic more obvious (thanks to @nuwang). Pull Request 12360
- Fix variable name typo in watchers (thanks to @nuwang). Pull Request 12368
- FastAPI: deprecate url attribute (again) (thanks to @davelopez). Pull Request 12370
- Avoid parsing the entire form model to the form display wrapper Pull Request 12374
- Remove tool_conf.xml.main which is no longer used (thanks to @nuwang). Pull Request 12380
- Removing unused
poolsize
argument from code and config. (thanks to @kxk302). Pull Request 12381 - FastAPI: support reverse URL lookups (thanks to @davelopez). Pull Request 12391
- Adapt quotas tests to use JSON payload (thanks to @davelopez). Pull Request 12417
- Declarative mapping follow-up: model constructors cleanup Pull Request 12424
- Vuefy show_params.mako (thanks to @OlegZharkov). Pull Request 12432
- Return tool_name only when show_job is full (thanks to @OlegZharkov). Pull Request 12457
- Drop unused models: DeferredJob and TransferJob Pull Request 12461
- Drop bcftools requirement from set_metadata tool Pull Request 12472
- Revert “Install Tempita from a fork due to use_2to3 deprecation” (thanks to @nsoranzo). Pull Request 12504
- FastAPI: explicitly return empty response with 204 status (thanks to @davelopez). Pull Request 12505
- Modernize sorter (sort1) tool Pull Request 12619
- Rephrase and fix typos (thanks to @simonbray). Pull Request 12750
- Add missing tool_ids to workflow invocation failure message (thanks to @simonbray). Pull Request 12823
- Add docker image auto-building in github workflow (thanks to @almahmoud). Pull Request 12520
Fixes¶
- Fix
_get_reference_data
method signature Pull Request 12562 - Fix new user welcome plugin build status storage/detection Pull Request 12779
- Fix msa visualization Pull Request 12782
- Fix edta metadata setting (thanks to @bernt-matthias). Pull Request 12273
- Increase specificity of mothur.pair.dist sniffer (thanks to @bernt-matthias). Pull Request 12280
- Small fix in binary.py (thanks to @melibleq). Pull Request 12384
- Fix cmap sniffer (thanks to @astrovsky01). Pull Request 12509
- Add file_ext property to Pretext and others datatypes (thanks to @bernt-matthias). Pull Request 12713
- Make vg a subclass of CompressedArchive (thanks to @bernt-matthias). Pull Request 12718
- Fix typo in interactivetool_jupyter_notebook.xml help section (thanks to @maximskorik). Pull Request 12077
- Update interactivetool_pyiron.xml (thanks to @gmauro). Pull Request 12127
- Fix patterns in Grep1 tool Pull Request 12166
- Restore Grep1 version 1.0.1 Pull Request 12252
- Add switch for optional select in workflow editor Pull Request 12138
- Do not persist tool state when invoking workflow Pull Request 12141
- Fix failure to serialize invocation / drop stored_workflow_id from invocation API Pull Request 12148
- Fix various TRS bugs and add tests Pull Request 12182
- Fix simplified workflow run form config setting Pull Request 12204
- Fix expanding collections in invocation view Pull Request 12216
- Disable text input for unselected inputs Pull Request 12640
- Flush new history before adding items Pull Request 12771
- Swap to galaxy fork of bootstrap-tour Pull Request 12210
- Beta history annotation, title, and tag editor Pull Request 12299
- Fix typo in docs Pull Request 12450
- Handle k8s job creation failures (thanks to @brinkmanlab). Pull Request 11715
- More IT and k8s runner fixes (thanks to @almahmoud). Pull Request 11989
- Unquote globs in from_work_dir ouptuts Pull Request 12049
- Quote extract_dataset_parts.sh call for parallelism mechanism (thanks to @bernt-matthias). Pull Request 12183
- Fix crash when uwsgi + mules has unhandled jobs at startup Pull Request 12215
- Handle metadata explicitly in kubernetes job runner instead of relying on legacy fallback (thanks to @nuwang). Pull Request 12243
- Fix version command when using extended metadata Pull Request 12245
- Fix composite inputs when using Pulsar. Pull Request 12259
- Fix Pulsar dynamic output discovery for various simple tool specified patterns. Pull Request 12260
- Added additional guard conditions in k8s runner to prevent KeyError (thanks to @nuwang). Pull Request 12277
- Fix Pulsar’s ability to read tool provided metadata when path is overridden. Pull Request 12284
- Continue handler startup even if job working directory can’t be recovered Pull Request 12316
- Fix sample job_config file to reflect that tmp_dir can be an expression or the string
True
(thanks to @nuwang). Pull Request 12361 - Fail data manager job when processing table entry fails Pull Request 12495
- Delay start of job runners Pull Request 12575
- Fix double enqueuing of upload jobs Pull Request 12763
- Use correct path for cgroup metrics when running within containers (thanks to @nuwang). Pull Request 12792
- Fix documentation for ftp_upload_dir and ftp_upload_site setting (thanks to @lldelisle). Pull Request 12164
- Fix non-closing masthead dropdown (thanks to @OlegZharkov). Pull Request 11962
- Update tensorflow to 2.5.0. Pull Request 12026
- Fix query parameter in /api/libraries/{id}/permissions (thanks to @davelopez). Pull Request 12047
- Add/drop index together with job_id column (thanks to @nsoranzo). Pull Request 12050
- Fix pysam.view call (thanks to @bernt-matthias). Pull Request 12061
- Open partfile in rb-mode in multipart uploading (thanks to @bioflowy). Pull Request 12084
- Make markdown components for reports and pages full width (thanks to @hexylena). Pull Request 12085
- Fix history audit table row trigger Pull Request 12130
- Update FastAPI to 0.65.2 and dependencies (thanks to @davelopez). Pull Request 12136
- Fix subworkflow tool state upgrade parsing Pull Request 12139
- Add test cases for collection builder dialogs (thanks to @assuntad23). Pull Request 12154
- Fix remote file upload if Galaxy is served under a prefix (thanks to @almahmoud). Pull Request 12155
- Add timeout to all urlopen and requests.* methods Pull Request 12173
- Allow
decompress="true"
in test comparison methods Pull Request 12187 - Fix TRS search if search term contains - Pull Request 12196
- Allow leading whitespace in TRS search term Pull Request 12197
- Add closing slash in tool schema documentation for
has_size
attribute (thanks to @bernt-matthias). Pull Request 12206 - Work around null hid Pull Request 12217
- Assorted fixes to debugging documentation Pull Request 12218
- Don’t let reports auto-create database tables Pull Request 12220
- Small fixes for beta history panel. Pull Request 12228
- Fix fugue pencil on old sharing not showing up correctly. Pull Request 12235
- Fix string formatting bug in test interactor Pull Request 12253
- Added check to install ‘fs.sshfs’ package (thanks to @kjetilkl). Pull Request 12269
- Fix type of
page
andpage_limit
in Libraries Folder permissions (thanks to @OlegZharkov). Pull Request 12271 - Improve handling of unexpected values in is_empty_file Pull Request 12275
- Beta history: Dataset Collection API fix for updating tags Pull Request 12286
- Allow scrolling in autocomplete options, fix search word filtering Pull Request 12290
- Add a GDPR-friendly user purge to pgcleanup Pull Request 12293
- Fix admin user manage Pull Request 12295
- Reword history import button text (thanks to @bernt-matthias). Pull Request 12304
- Fix order of dataset instances in dataset collection Pull Request 12305
- Fix recursive file list in posix remote files (thanks to @OlegZharkov). Pull Request 12307
- Linter support for
format_source
in static collection elements (thanks to @bernt-matthias). Pull Request 12309 - Make authnz
end_session_endpoint
optional (thanks to @nuwang). Pull Request 12311 - Use workflow step title as defined in the workflow model Pull Request 12320
- Gitlab Error report - Remove previously required urllib (thanks to @selten). Pull Request 12333
- Identify tool by name, owner, toolshed (thanks to @pvanheus). Pull Request 12338
- Fix for empty docker_volumes/singularity_volumes in job config Pull Request 12341
- Fix up plugin_config module modifying configuration dictionaries. Pull Request 12354
- Remove NetworkException catch clauses in iRODS object store (thanks to @kxk302). Pull Request 12363
- Bump tensorflow from 2.5.0 to 2.5.1 in /lib/galaxy/dependencies Pull Request 12378
- Added missing triggers package to galaxy data (thanks to @nuwang). Pull Request 12389
- Fix hids, alignment, other style issues in beta history. Pull Request 12406
- Fixes to selenium testing with beta history panel enabled. Pull Request 12407
- Downgrade Cheetah3 to 3.2.6.post1 (thanks to @nsoranzo). Pull Request 12408
- Install Tempita from a fork due to use_2to3 deprecation (thanks to @nsoranzo). Pull Request 12413
- Fix flaky failing workflow editor selenium test. Pull Request 12423
- Bump sqlparse from 0.4.1 to 0.4.2 in /lib/galaxy/dependencies Pull Request 12436
- Fix keycloak user creation username handling. Pull Request 12444
- Make Role description field optional (thanks to @davelopez). Pull Request 12447
- Drop symlink to tool_conf.xml.main Pull Request 12451
- Fix history contents API update batch with collections (thanks to @davelopez). Pull Request 12456
- Remove default pagination in LibraryPopulator.get_permissions() (thanks to @davelopez). Pull Request 12463
- Drop tool_name from dataset details Pull Request 12465
- Strip whitespace on urls when uploading (thanks to @assuntad23). Pull Request 12474
- Remove default value string from
/api/genomes
endpoint (thanks to @assuntad23). Pull Request 12481 - Explicitly set page_limit in test_get_library_available_permissions (thanks to @davelopez). Pull Request 12483
- Update dataset edit toggle button to refer to dataset instead of coll… Pull Request 12485
- Handle deleted panel views in the UI. Pull Request 12488
- Fix bug when restarting Galaxy in selenium integration tests. Pull Request 12489
- Remove invalid syntax from tool schema (thanks to @bernt-matthias). Pull Request 12494
- Add PostgreSQL < 9.5 deprecation notice to 21.05 release announce (thanks to @nsoranzo). Pull Request 12496
- Fix indention for admin panel links Pull Request 12497
- Add profile that strips whitespace in from_work_dir outputs Pull Request 12536
- Respect tool version in verify_tool Pull Request 12539
- Catch datatype conversion exception and return proper error Pull Request 12561
- Fix async controller Pull Request 12565
- Fix scratchbook on dataset details pages (thanks to @OlegZharkov). Pull Request 12566
- Drop special-casing of current Galaxy version for news webhook Pull Request 12579
- Fix a small bug in Error summary Vue template. Pull Request 12581
- Avoid uncaught exceptions when trying to set invalid tag names (thanks to @davelopez). Pull Request 12582
- Fix job detail caching Pull Request 12586
- Fix output state handling, disable connectivity for conditionals Pull Request 12591
- Sync reset mapping with Node component map-over state Pull Request 12598
- Remove Interactive Environments from Visualizations Pull Request 12599
- Fix file source restrictions (thanks to @davelopez). Pull Request 12607
- Fix branch for release notes (thanks to @hexylena). Pull Request 12615
- Fix: encode all ids when returning a ldda in datasets API show operation (thanks to @davelopez). Pull Request 12616
- Fix history export link copy Pull Request 12618
- Fix collection replacement and job resuming when re-running single ma… Pull Request 12621
- Allow users to retry tool job submissions if an error occurs Pull Request 12623
- Restore overwritten styles Pull Request 12624
- Allow empty truevalue for conditional test parameters Pull Request 12625
- Dispose previously mounted Vue-components in Analysis router Pull Request 12627
- Fix new user welcome styles Pull Request 12630
- Fix id encoding in datasets API show method (thanks to @nsoranzo). Pull Request 12634
- Add property to disable tool form Pull Request 12645
- Move node update requests to workflow component Pull Request 12648
- Fix directory_uri tool parameter validation error (thanks to @davelopez). Pull Request 12653
- Ensure that tool installations use the default tool panel Pull Request 12655
- Show loading error in tool form Pull Request 12669
- Fix possible
None
in TokenContainedEvaluator (thanks to @davelopez). Pull Request 12675 - Reduce number of Tool Form requests in Workflow Editor, improve visibility of Tool Infos Pull Request 12702
- Continue deleting dataset collection if member HDA has no history Pull Request 12722
- Fix for PairedListCreator errant autopairing (thanks to @assuntad23). Pull Request 12727
- Various show page PDF bug fixes. Pull Request 12728
- Fix linter: Parameter validator needs no expression (thanks to @bernt-matthias). Pull Request 12733
- Fix chrome scrolling on insert in markdown editor Pull Request 12737
- Two fixes for linting (thanks to @bernt-matthias). Pull Request 12757
- Prefer model class when it exists in grid sorting Pull Request 12758
- Use default alert info instead of custom small info style Pull Request 12764
- Drop legacy_expose_api from api/datasets Pull Request 12795
- Use
post
instead ofput
to create copy of dataset collection Pull Request 12796 - Allow sessionless access to genomes API (thanks to @nsoranzo). Pull Request 12799
- Fix wrong dataset details link Pull Request 12805
- Disable library uploads using master API key Pull Request 12806
- Add missing tool_ids to workflow invocation failure message (thanks to @simonbray). Pull Request 12823
- Allow dataset and dataset collection deletion for anonymous users Pull Request 12817
- Fix
from_work_dir
glob with extended metadata and pulsar Pull Request 12816 - Fix remote object store datasets not purged Pull Request 12815
- Pin a resolution for ua-parser-js to 0.7.30 Pull Request 12827
- Allow sessionless access to some datasets API endpoints (thanks to @nsoranzo). Pull Request 12830
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