mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 00:12:08 +08:00
Merge branch 'release_25.1' into dev
This commit is contained in:
mvdbeek
@@ -1,6 +1,118 @@
|
||||
|
||||
:orphan:
|
||||
|
||||
===========================================================
|
||||
25.1 Galaxy Release
|
||||
25.1 Galaxy Release (December 2025)
|
||||
===========================================================
|
||||
|
||||
.. include:: _header.rst
|
||||
|
||||
Please see the `25.1 user release notes <25.1_announce_user.html>`__ for a summary of new user features.
|
||||
The `GitHub Release Notes <https://github.com/galaxyproject/galaxy/releases/tag/v25.1.0>`__ provide a comprehensive overview of all changes.
|
||||
|
||||
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_25.1 https://github.com/galaxyproject/galaxy.git
|
||||
|
||||
To update an existing Galaxy repository run:
|
||||
.. code-block:: shell
|
||||
|
||||
$ git fetch origin && git checkout release_25.1 && git pull --ff-only origin release_25.1
|
||||
|
||||
See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details on source code locations.
|
||||
|
||||
|
||||
Admin Notes
|
||||
===========================================================
|
||||
|
||||
**Database Migrations will require stopping the Galaxy instance**
|
||||
This release includes database migrations that require the Galaxy instance to be stopped
|
||||
before applying the update. Please plan accordingly to minimize downtime for users.
|
||||
|
||||
Configuration Changes
|
||||
===========================================================
|
||||
|
||||
|
||||
Added
|
||||
-----
|
||||
|
||||
The following configuration options are new
|
||||
|
||||
config/galaxy.yml.sample:galaxy
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
- mapping.tool_shed.mapping.allow_local_account_creation
|
||||
|
||||
|
||||
Removed
|
||||
-------
|
||||
|
||||
The following configuration options have been completely removed
|
||||
|
||||
config/galaxy.yml.sample:galaxy
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
- mapping.tool_shed.mapping.allow_user_creation
|
||||
|
||||
|
||||
Deprecation Notices
|
||||
===========================================================
|
||||
|
||||
**Deprecation of the Trackster Visualization in Galaxy release 26.0**
|
||||
The legacy Trackster genome browser visualization has been deprecated and
|
||||
`will be completely removed in Galaxy 26.0 <https://github.com/galaxyproject/galaxy/pull/20974>`__. This includes
|
||||
the removal of special handling for Trackster across tool execution, toolbox filtering, visualization
|
||||
framework features, controller endpoints, client code, and other conditional logic. With the removal of
|
||||
Trackster, the era of Mako-based visualizations served from controller endpoints ends.
|
||||
Galaxy now provides the modern IGV (Integrative Genomics Viewer) as the primary genome browser
|
||||
visualization, offering superior functionality and performance for genomic data exploration.
|
||||
|
||||
**Deprecation of Mako-based visualizations in Galaxy release 26.0**
|
||||
With the removal of Trackster in 26.0, the remaining legacy Mako-based visualization framework
|
||||
and controller endpoints are deprecated and
|
||||
`will be completely removed in Galaxy 26.0 <https://github.com/galaxyproject/galaxy/pull/21133>`__.
|
||||
Any remaining Mako-based visualizations should be migrated to the modern script-based visualization
|
||||
plugin framework. Users and administrators are encouraged to transition to supported visualization
|
||||
plugins to ensure continued functionality and access to new features.
|
||||
|
||||
**Deprecation of the Galaxy Reports application in Galaxy release 26.0**
|
||||
The standalone Galaxy Reports application, which provides administrative usage statistics and
|
||||
analytics for Galaxy instances, is deprecated and will be removed in Galaxy 26.0.
|
||||
The Reports app was a separate web application that connected to the Galaxy database to display
|
||||
information about jobs, workflows, users, and system usage. Administrators currently using the
|
||||
Reports app should plan to migrate to alternative monitoring and analytics solutions before
|
||||
Galaxy 26.0 is released next year. The following GTN tutorials provide guidance on alternative
|
||||
monitoring approaches:
|
||||
|
||||
* `Galaxy Monitoring with Telegraf and Grafana <https://training.galaxyproject.org/training-material/topics/admin/tutorials/monitoring/tutorial.html>`__
|
||||
* `Galaxy Monitoring with gxadmin <https://training.galaxyproject.org/training-material/topics/admin/tutorials/gxadmin/tutorial.html>`__
|
||||
|
||||
Release Team
|
||||
===========================================================
|
||||
|
||||
Release manager: `Ahmed Awan <https://github.com/ahmedhamidawan>`__, `Aysam Guerler <https://github.com/guerler>`__
|
||||
|
||||
Release testing:
|
||||
|
||||
* `Tyler Collins <https://github.com/tcollins2011>`__
|
||||
* `Arash Kadkhodaei <https://github.com/arash77>`__
|
||||
* `John Chilton <https://github.com/jmchilton>`__
|
||||
* `Keith Suderman <https://github.com/ksuderman>`__
|
||||
* `Aysam Guerler <https://github.com/guerler>`__
|
||||
* `Alireza Heidari <https://github.com/itisAliRH>`__
|
||||
* `Jennifer Hillman-Jackson <https://github.com/jennaj>`__
|
||||
|
||||
Communications:
|
||||
|
||||
* `Natalie Whitaker-Allen <https://github.com/natalie-wa>`__
|
||||
* `Scott Cain <https://github.com/scottcain>`__
|
||||
|
||||
A special thank you goes to everyone who helped test the new release after its deployment on usegalaxy.org.
|
||||
|
||||
----
|
||||
|
||||
.. include:: _thanks.rst
|
||||
|
||||
@@ -0,0 +1,456 @@
|
||||
|
||||
===========================================================
|
||||
25.1 Galaxy Release (October 2025)
|
||||
===========================================================
|
||||
|
||||
.. include:: _header.rst
|
||||
|
||||
Please see the full `release notes <https://github.com/galaxyproject/galaxy/releases/tag/v25.1.0>`__ for more details.
|
||||
|
||||
Highlights
|
||||
===========================================================
|
||||
|
||||
Discover some of the exciting new features, enhancements, and improvements in Galaxy 25.1.
|
||||
|
||||
A Fresh, Modern History List Interface
|
||||
--------------------------------------
|
||||
|
||||
Galaxy 25.1 introduces a redesigned history list that makes managing your histories more intuitive and
|
||||
visually appealing.
|
||||
|
||||
- **Card-based design**. Histories are now displayed as clean, modern cards that provide better visual
|
||||
organization in a grid vs list view, as you prefer.
|
||||
- **Enhanced information display**. Each history card shows key details at a glance, including
|
||||
creation date, size, update time, and status indicators in a more structured layout.
|
||||
- **Improved responsive design**. The new interface adapts better to different screen sizes and
|
||||
provides a more consistent experience across devices.
|
||||
- **Advanced keyboard navigation and selection**. Navigate through histories using arrow keys,
|
||||
select multiple histories with Shift+click for range selection, and use keyboard shortcuts
|
||||
for efficient bulk operations — available across multiple Galaxy list interfaces.
|
||||
|
||||
This update modernizes one of Galaxy's core interfaces, providing a cleaner and more user-friendly
|
||||
way to navigate your analysis history collection while adding powerful selection capabilities.
|
||||
[`#20744 <https://github.com/galaxyproject/galaxy/pull/20744>`__]
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/1kPTyiEr3ks?si=OYLxFeyA82bZ13Xd" title="Galaxy 25.1 - A Fresh, Modern History List Interface" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
|
||||
|
||||
Smart Sample Sheets for Complex Workflow Inputs
|
||||
-----------------------------------------------
|
||||
|
||||
Galaxy now supports **Sample Sheets** to simplify complex workflow inputs and data organization. This
|
||||
feature allows you to import data from external spreadsheets (CSV, TSV, or Excel) and use them to
|
||||
configure workflow parameters and organize datasets.
|
||||
|
||||
- **Spreadsheet-style data entry**. Define your experimental data using familiar spreadsheet interfaces
|
||||
with customizable columns for sample names, treatments, conditions, and file locations — whether
|
||||
datasets or remote URLs.
|
||||
- **Workflow author-defined templates**. Workflow creators can pre-configure sample sheet templates
|
||||
with specific columns, validation rules, and helpful descriptions, guiding users through proper data
|
||||
organization.
|
||||
- **Built into the Apply Rules tool**. Advanced users can leverage sample sheet data within the Apply
|
||||
Rules tool for sophisticated data manipulation and collection operations.
|
||||
- **Integration within the Workflow Editor**. Configure workflows to accept sample sheet inputs
|
||||
directly from the Workflow Editor.
|
||||
|
||||
Sample Sheets are particularly useful for workflows that require multiple related inputs or when you
|
||||
need to process batches of samples with associated metadata in a structured format.
|
||||
[`#19305 <https://github.com/galaxyproject/galaxy/pull/19305>`__]
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/5sAjEABPh8M?si=sxIX6RV1LtUkH4xW" title="Galaxy 25.1 - Smart Sample Sheets for Complex Workflow Inputs" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
|
||||
|
||||
An Enhanced Tool Discovery View
|
||||
-------------------------------
|
||||
|
||||
Galaxy 25.1 introduces a redesigned **Tool Discovery View** that replaces the previous advanced tool
|
||||
search with a more powerful and intuitive tool exploration interface.
|
||||
|
||||
- **Dedicated Discovery Interface**. Advanced tool search has moved from the tool panel to a rich,
|
||||
dedicated center-panel view optimized for finding the right tools for your analysis.
|
||||
- **Card-based Tool Display**. Tools are presented as visually appealing cards with key information,
|
||||
including EDAM ontology tags, descriptions, and links.
|
||||
- **Tool Favorites and Sharing**. Easily add tools to your favorites for quick access, and share useful
|
||||
tools with colleagues via the copyable link feature.
|
||||
- **EDAM Ontology Integration**. Browse and filter tools by EDAM (EMBRACE Data and Methods) ontologies
|
||||
to discover tools based on scientific domains and data types.
|
||||
|
||||
This new interface makes tool discovery more efficient and helps users find the most appropriate tools
|
||||
for their specific analysis needs.
|
||||
[`#20747 <https://github.com/galaxyproject/galaxy/pull/20747>`__]
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/7L_QjcwyBiw?si=gD8tGTr0BTzgv7rw" title="Galaxy 25.1 - Tool Discovery View" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
|
||||
|
||||
New Galaxy Charts Visualization Framework
|
||||
-----------------------------------------
|
||||
|
||||
This release also introduces the **Galaxy Charts** framework, bringing enhanced visualizations and a
|
||||
more powerful visualization experience to Galaxy users.
|
||||
|
||||
- **Improved Visualization Performance**. Enjoy faster loading times, smoother interactions, and more
|
||||
responsive visualizations built with modern web technologies for a better user experience.
|
||||
- **Enhanced IGV.js Genome Browser**. Galaxy now includes a complete IGV.js (Integrative Genome Browser)
|
||||
integration for comprehensive genomic data visualization with multi-track support for BAM, VCF,
|
||||
BigWig, BED, GFF, GTF, and CRAM files.
|
||||
- **Automatic Data Integration**. Visualizations now automatically connect to your Galaxy datasets and
|
||||
match reference genomes, eliminating manual configuration steps and making it easier to explore your
|
||||
data.
|
||||
- **Expanded Visualization Library**. The new framework enables rapid deployment of cutting-edge
|
||||
visualizations, meaning Galaxy users will see more powerful visualization options in future releases.
|
||||
|
||||
*See the Admin Notes and Deprecation Notices sections* :doc:`here <25.1_announce>` *for more details on
|
||||
the visualization framework and the removal of Trackster.*
|
||||
|
||||
**Featured Implementation: IGV.js Genome Browser**
|
||||
|
||||
Galaxy 25.1 ships with a complete IGV.js (Integrative Genome Browser) implementation built on the
|
||||
Galaxy Charts framework, showcasing the platform's capabilities:
|
||||
|
||||
- **Multi-track Genomic Visualization**. View multiple tracks in various formats including BAM, VCF,
|
||||
BigWig, BED, GFF, GTF, and CRAM files with full support for indexed data and byte-range requests.
|
||||
- **Automatic Genome Matching**. Automatically matches dataset database keys against available genomes,
|
||||
supporting both IGV-provided reference genomes and Galaxy-served genomes in 2bit and FASTA formats.
|
||||
- **Interactive Exploration**. Full IGV.js functionality including zooming, panning, dynamic track
|
||||
configuration, and multi-sample comparisons for comprehensive genomic data analysis.
|
||||
|
||||
The Galaxy Charts framework represents a major advancement in Galaxy's visualization capabilities,
|
||||
making it easier than ever to create sophisticated, interactive visualizations while maintaining full
|
||||
integration with Galaxy's data management and analysis ecosystem. Here's a look at the IGV.js addition:
|
||||
[`#20943 <https://github.com/galaxyproject/galaxy/pull/20943>`__]
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/VC05IvZGPiU?si=tMVdiHS1d5yTOX06" title="Galaxy 25.1 - New Galaxy Charts Visualization Framework" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
|
||||
|
||||
A Place to Find your Recent Downloads in Galaxy
|
||||
-----------------------------------------------
|
||||
|
||||
Galaxy 25.1 introduces a dedicated "Recent Exports & Downloads" page that lists your recent
|
||||
exports/downloads.
|
||||
|
||||
- **Re-download available items**. Easily access and download files still available in the short-term
|
||||
storage cache.
|
||||
- **Navigate to source objects**. Jump directly to the details page of the originating item (e.g.
|
||||
workflow invocation, history, etc.).
|
||||
|
||||
This improves the discoverability and accessibility of recent downloads without needing to track links
|
||||
manually.
|
||||
[`#20585 <https://github.com/galaxyproject/galaxy/pull/20585>`__]
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/NMeH_HWuMwA?si=ly9gCTQksghLwRf0" title="Galaxy 25.1 - A Place to Find your Recent Downloads in Galaxy" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
|
||||
|
||||
Visual Indicators for Short-Term Storage Expiration
|
||||
---------------------------------------------------
|
||||
|
||||
Galaxy 25.1 introduces visual expiration indicators that help users identify when datasets and
|
||||
collections are stored in temporary or short-term storage that will be automatically cleaned up.
|
||||
|
||||
- **Expiration warnings in history**. Datasets and collections now display countdown timers showing
|
||||
when they will expire, helping users plan data management and downloads before automatic cleanup.
|
||||
- **Collection-aware indicators**. Smart detection across dataset collections shows the earliest
|
||||
expiration time when collections contain datasets from mixed storage types.
|
||||
- **Admin-configurable expiration periods**. Administrators can set `object_expires_after_days` in
|
||||
object store configurations to match their actual cleanup schedules and inform users appropriately.
|
||||
|
||||
*Note that Galaxy instance administrators must set `object_expires_after_days` in their object store
|
||||
configurations for these indicators to function correctly.*
|
||||
|
||||
This feature is particularly valuable for instances using scratch storage or temporary
|
||||
high-performance storage tiers, as it gives users clear visibility into data lifecycle and helps
|
||||
prevent unexpected data loss due to automatic cleanup processes.
|
||||
[`#20332 <https://github.com/galaxyproject/galaxy/pull/20332>`__]
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/CytCTixQTY8?si=taaSIrbl_gM2QhUC" title="Galaxy 25.1 - Visual Indicators for Short-Term Storage Expiration" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
|
||||
|
||||
Galaxy Tools Now Handle Secrets and Authentication
|
||||
--------------------------------------------------
|
||||
|
||||
Galaxy 25.1 implements a comprehensive tool credentials system, allowing tools to securely access
|
||||
external services by defining authentication credentials (variables and secrets) in tool requirements
|
||||
while keeping sensitive information separate from tool definitions.
|
||||
|
||||
- **Credential Definition in Tools**. Tools can define credential requirements using `<credentials>`
|
||||
elements within `<requirements>` with support for both variables (non-sensitive config like URLs,
|
||||
usernames) and secrets (sensitive data like passwords, API keys).
|
||||
- **Secure Storage & Management**. Integration with Galaxy's vault system provides secure secret
|
||||
storage with user-specific credential isolation by tool and service, plus credential groups for
|
||||
organizing multiple credential sets.
|
||||
- **REST API**. Complete CRUD operations enable credential management with user credential listing,
|
||||
group-based credential organization, and secure deletion with vault cleanup.
|
||||
- **Frontend Integration**. Unified credential management UI appears for every tool with workflow-level
|
||||
credential status display, multi-tool credential coordination, and real-time credential validation
|
||||
and feedback.
|
||||
- **Tool Execution Integration**. Automatic credential injection as environment variables with job
|
||||
context tracking for credential usage, supporting tool proxies and various tool types while
|
||||
maintaining backward compatibility.
|
||||
|
||||
This system provides secure credential management for tools that need to access external APIs,
|
||||
databases, or cloud services, ensuring sensitive authentication information is properly protected
|
||||
while making it easy for users to configure and manage their credentials across different tools and
|
||||
workflows.
|
||||
[`#19084 <https://github.com/galaxyproject/galaxy/pull/19084>`__]
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/2xEFtTS3DSk?si=TvG5EUBy96Otrt9T" title="Galaxy 25.1 - Tools Now Handle Secrets and Authentication" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
|
||||
|
||||
Search for Steps, Tools and Subworkflows within the Workflow Editor
|
||||
-------------------------------------------------------------------
|
||||
|
||||
As with many improvements to the Workflow Editor in recent releases, Galaxy 25.1 adds the ability to
|
||||
search for several properties of all elements in the workflow graph, displays the search results in a
|
||||
list, and highlights them when clicked.
|
||||
[`#20390 <https://github.com/galaxyproject/galaxy/pull/20390>`__]
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/Guma5nPqZ_8?si=BuQ2xkiCCULhV_Q5" title="Galaxy 25.1 - A Search in the Workflow Editor" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
|
||||
|
||||
A Redesign of your User Preferences
|
||||
-----------------------------------
|
||||
|
||||
The User Preferences interface has been redesigned to enhance user experience through improved
|
||||
navigation and a modernised interface.
|
||||
[`#19658 <https://github.com/galaxyproject/galaxy/pull/19658>`__]
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/vTjJtStlf9w?si=98P65gcBJP0xNDZA" title="Galaxy 25.1 - A Redesign of your User Preferences" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
|
||||
|
||||
----
|
||||
|
||||
Visualizations Updates
|
||||
===========================================================
|
||||
|
||||
.. visualizations
|
||||
* [igv] Allow selection of genomes from history fasta/2bit
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 21269`_
|
||||
* Add Hyphy Vision Result Viewer
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 21196`_
|
||||
* Enable drag-and-drop of collection elements in IGV
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 21173`_
|
||||
* Update Javascript package licenses to MIT
|
||||
(thanks to `@mr-c <https://github.com/mr-c>`__).
|
||||
`Pull Request 20264`_
|
||||
* Install Visualization plugins as self-contained packages
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20348`_
|
||||
* Restore Nora
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20387`_
|
||||
* Install visualizations directly to static path, avoid duplication
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20372`_
|
||||
* Add rerun.io web viewer
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20202`_
|
||||
* Update tiffviewer visualization to version 0.0.3
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 20658`_
|
||||
* Consolidate visualization mako, avoid user agent styles
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20760`_
|
||||
* Enable data label column selection in basic Plotly plots and add heatmap
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20813`_
|
||||
* Update JupyterLite version to 0.6.4
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20877`_
|
||||
* Add Multiple Sequence Alignment Viewer 2.0
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20907`_
|
||||
* Make jupyterlite default visualization for ipynb
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20931`_
|
||||
* Fix JupyterLite History Identifier Retrieval Without Dataset
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20971`_
|
||||
* Save IGV locus and improve error handling
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20996`_
|
||||
* Bump vitessce to 3.8.2
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 21003`_
|
||||
* Fix and migrate HIV-TRACE to Charts Visualization Framework
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 21006`_
|
||||
* Add README and update the minimal visualization example
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 21007`_
|
||||
* Allow creation of visualizations without dataset
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20914`_
|
||||
* Adds IGV.js Visualization
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 20943`_
|
||||
|
||||
Datatypes Updates
|
||||
===========================================================
|
||||
|
||||
.. datatypes
|
||||
* New datatype addition: HAL
|
||||
(thanks to `@SaimMomin12 <https://github.com/SaimMomin12>`__).
|
||||
`Pull Request 21379`_
|
||||
* Add PNTS datatype for 3D Tiles Point Cloud
|
||||
(thanks to `@kgerb <https://github.com/kgerb>`__).
|
||||
`Pull Request 21414`_
|
||||
* Backport fix anndata datatype update
|
||||
(thanks to `@nilchia <https://github.com/nilchia>`__).
|
||||
`Pull Request 21111`_
|
||||
* Fix MIME type for LAZ datatype
|
||||
(thanks to `@kysrpex <https://github.com/kysrpex>`__).
|
||||
`Pull Request 21202`_
|
||||
* Add SpatialData datatype
|
||||
(thanks to `@nilchia <https://github.com/nilchia>`__).
|
||||
`Pull Request 21000`_
|
||||
* support ZARR v3 for Spatialdata dt
|
||||
(thanks to `@nilchia <https://github.com/nilchia>`__).
|
||||
`Pull Request 21265`_
|
||||
* Fix forward merge
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 21307`_
|
||||
* Fix tool-provided metadata for CONVERTER_tar_to_directory
|
||||
(thanks to `@mr-c <https://github.com/mr-c>`__).
|
||||
`Pull Request 20260`_
|
||||
* Pin isa-rwval 0.10.11, drop conditional import handling
|
||||
(thanks to `@natefoo <https://github.com/natefoo>`__).
|
||||
`Pull Request 20527`_
|
||||
* Remove ``num_unique_values`` tiff metadata element
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 20464`_
|
||||
* Add LocusZoom Visualization
|
||||
(thanks to `@elmedjadjirayane <https://github.com/elmedjadjirayane>`__).
|
||||
`Pull Request 20354`_
|
||||
* Add mzMLb and MBI datatypes
|
||||
(thanks to `@chambm <https://github.com/chambm>`__).
|
||||
`Pull Request 20632`_
|
||||
* Pairtool updated format and sniffers
|
||||
(thanks to `@Smeds <https://github.com/Smeds>`__).
|
||||
`Pull Request 20634`_
|
||||
* Add `num_unique_values` tiff metadata element, fixed
|
||||
(thanks to `@kostrykin <https://github.com/kostrykin>`__).
|
||||
`Pull Request 20669`_
|
||||
* add fasta.bz2 as auto_compressed type
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 20496`_
|
||||
* Add support for M4A audio files
|
||||
(thanks to `@arash77 <https://github.com/arash77>`__).
|
||||
`Pull Request 20667`_
|
||||
* Add datatype for LexicMap index
|
||||
(thanks to `@Smeds <https://github.com/Smeds>`__).
|
||||
`Pull Request 20586`_
|
||||
* Bump requirement of directory converters
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 20834`_
|
||||
* Undo accidental push
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 20854`_
|
||||
* Fix Ipynb datatype sniffer and add unit tests
|
||||
(thanks to `@ksuderman <https://github.com/ksuderman>`__).
|
||||
`Pull Request 20811`_
|
||||
* Add axt and maf to auto_compressed_types
|
||||
(thanks to `@richard-burhans <https://github.com/richard-burhans>`__).
|
||||
`Pull Request 20875`_
|
||||
* Add HiC datatype
|
||||
(thanks to `@abretaud <https://github.com/abretaud>`__).
|
||||
`Pull Request 20874`_
|
||||
* Fix DOCX detection and add PPTX support
|
||||
(thanks to `@arash77 <https://github.com/arash77>`__).
|
||||
`Pull Request 20827`_
|
||||
* Fix anndata metadata
|
||||
(thanks to `@nilchia <https://github.com/nilchia>`__).
|
||||
`Pull Request 20778`_
|
||||
* Use a streaming based parser (ijson) when setting metadata for biom1 files
|
||||
(thanks to `@ksuderman <https://github.com/ksuderman>`__).
|
||||
`Pull Request 20851`_
|
||||
* Add support for picking ``from_work_dir`` directory
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 20916`_
|
||||
* Skip sam metadata if we have too many references
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 20820`_
|
||||
* Extract: do not use common prefix dir
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 20929`_
|
||||
* Add Auspice JSON datatype
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
|
||||
`Pull Request 20466`_
|
||||
* Clean up code from pyupgrade
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 20642`_
|
||||
* Add safetensors datatype
|
||||
(thanks to `@nilchia <https://github.com/nilchia>`__).
|
||||
`Pull Request 20754`_
|
||||
* Add freq.json datatype subclass
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 21012`_
|
||||
* Merge 25.0 into dev
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 21018`_
|
||||
* New datatype addition: beast.trees datatype
|
||||
(thanks to `@SaimMomin12 <https://github.com/SaimMomin12>`__).
|
||||
`Pull Request 21055`_
|
||||
* New datatype addition: gam for vg toolkit
|
||||
(thanks to `@SaimMomin12 <https://github.com/SaimMomin12>`__).
|
||||
`Pull Request 21096`_
|
||||
* Prefix download link
|
||||
(thanks to `@martenson <https://github.com/martenson>`__).
|
||||
`Pull Request 21112`_
|
||||
* Add LAS and LAZ file format
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 21049`_
|
||||
* Add display_in_upload to LAZ and LAS
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 21060`_
|
||||
* Type annotation fixes for mypy 1.16.0
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 20424`_
|
||||
|
||||
Builtin Tool Updates
|
||||
===========================================================
|
||||
|
||||
.. tools
|
||||
* Set minimum profile version for expression tools
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 21151`_
|
||||
* Drop ucsc test server from sample build sites
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 20723`_
|
||||
* Drop Python helper script from sort1 tool
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 20876`_
|
||||
* Update requirements of sort1 tool
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 20892`_
|
||||
* Update maf tools with profiles, required_files, and requirements
|
||||
(thanks to `@natefoo <https://github.com/natefoo>`__).
|
||||
`Pull Request 20865`_
|
||||
* Modernize tools in the filters/ dir
|
||||
(thanks to `@natefoo <https://github.com/natefoo>`__).
|
||||
`Pull Request 20840`_
|
||||
* Add special case for BAM files in RStudio
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 20692`_
|
||||
* Fix comp1 / test_subworkflow_map_over_data_column
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 20992`_
|
||||
|
||||
Please see the full `release notes <https://github.com/galaxyproject/galaxy/releases/tag/v25.1.0>`__ for more details.
|
||||
The admin-facing release notes are available :doc:`here <25.1_announce>`.
|
||||
|
||||
.. include:: 25.1_prs.rst
|
||||
|
||||
----
|
||||
|
||||
.. include:: _thanks.rst
|
||||
@@ -0,0 +1,445 @@
|
||||
|
||||
.. github_links
|
||||
.. _Pull Request 21442: https://github.com/galaxyproject/galaxy/pull/21442
|
||||
.. _Pull Request 21435: https://github.com/galaxyproject/galaxy/pull/21435
|
||||
.. _Pull Request 21342: https://github.com/galaxyproject/galaxy/pull/21342
|
||||
.. _Pull Request 21269: https://github.com/galaxyproject/galaxy/pull/21269
|
||||
.. _Pull Request 21346: https://github.com/galaxyproject/galaxy/pull/21346
|
||||
.. _Pull Request 21349: https://github.com/galaxyproject/galaxy/pull/21349
|
||||
.. _Pull Request 21350: https://github.com/galaxyproject/galaxy/pull/21350
|
||||
.. _Pull Request 21379: https://github.com/galaxyproject/galaxy/pull/21379
|
||||
.. _Pull Request 21276: https://github.com/galaxyproject/galaxy/pull/21276
|
||||
.. _Pull Request 21360: https://github.com/galaxyproject/galaxy/pull/21360
|
||||
.. _Pull Request 21377: https://github.com/galaxyproject/galaxy/pull/21377
|
||||
.. _Pull Request 21414: https://github.com/galaxyproject/galaxy/pull/21414
|
||||
.. _Pull Request 21419: https://github.com/galaxyproject/galaxy/pull/21419
|
||||
.. _Pull Request 21426: https://github.com/galaxyproject/galaxy/pull/21426
|
||||
.. _Pull Request 21428: https://github.com/galaxyproject/galaxy/pull/21428
|
||||
.. _Pull Request 21191: https://github.com/galaxyproject/galaxy/pull/21191
|
||||
.. _Pull Request 21193: https://github.com/galaxyproject/galaxy/pull/21193
|
||||
.. _Pull Request 21196: https://github.com/galaxyproject/galaxy/pull/21196
|
||||
.. _Pull Request 21195: https://github.com/galaxyproject/galaxy/pull/21195
|
||||
.. _Pull Request 21111: https://github.com/galaxyproject/galaxy/pull/21111
|
||||
.. _Pull Request 21202: https://github.com/galaxyproject/galaxy/pull/21202
|
||||
.. _Pull Request 21197: https://github.com/galaxyproject/galaxy/pull/21197
|
||||
.. _Pull Request 21192: https://github.com/galaxyproject/galaxy/pull/21192
|
||||
.. _Pull Request 21214: https://github.com/galaxyproject/galaxy/pull/21214
|
||||
.. _Pull Request 21203: https://github.com/galaxyproject/galaxy/pull/21203
|
||||
.. _Pull Request 21210: https://github.com/galaxyproject/galaxy/pull/21210
|
||||
.. _Pull Request 21212: https://github.com/galaxyproject/galaxy/pull/21212
|
||||
.. _Pull Request 21023: https://github.com/galaxyproject/galaxy/pull/21023
|
||||
.. _Pull Request 21223: https://github.com/galaxyproject/galaxy/pull/21223
|
||||
.. _Pull Request 21233: https://github.com/galaxyproject/galaxy/pull/21233
|
||||
.. _Pull Request 21213: https://github.com/galaxyproject/galaxy/pull/21213
|
||||
.. _Pull Request 21232: https://github.com/galaxyproject/galaxy/pull/21232
|
||||
.. _Pull Request 21000: https://github.com/galaxyproject/galaxy/pull/21000
|
||||
.. _Pull Request 21246: https://github.com/galaxyproject/galaxy/pull/21246
|
||||
.. _Pull Request 21240: https://github.com/galaxyproject/galaxy/pull/21240
|
||||
.. _Pull Request 21249: https://github.com/galaxyproject/galaxy/pull/21249
|
||||
.. _Pull Request 21200: https://github.com/galaxyproject/galaxy/pull/21200
|
||||
.. _Pull Request 21274: https://github.com/galaxyproject/galaxy/pull/21274
|
||||
.. _Pull Request 21265: https://github.com/galaxyproject/galaxy/pull/21265
|
||||
.. _Pull Request 21282: https://github.com/galaxyproject/galaxy/pull/21282
|
||||
.. _Pull Request 21284: https://github.com/galaxyproject/galaxy/pull/21284
|
||||
.. _Pull Request 21280: https://github.com/galaxyproject/galaxy/pull/21280
|
||||
.. _Pull Request 21293: https://github.com/galaxyproject/galaxy/pull/21293
|
||||
.. _Pull Request 21013: https://github.com/galaxyproject/galaxy/pull/21013
|
||||
.. _Pull Request 21290: https://github.com/galaxyproject/galaxy/pull/21290
|
||||
.. _Pull Request 21294: https://github.com/galaxyproject/galaxy/pull/21294
|
||||
.. _Pull Request 21314: https://github.com/galaxyproject/galaxy/pull/21314
|
||||
.. _Pull Request 21307: https://github.com/galaxyproject/galaxy/pull/21307
|
||||
.. _Pull Request 21261: https://github.com/galaxyproject/galaxy/pull/21261
|
||||
.. _Pull Request 21273: https://github.com/galaxyproject/galaxy/pull/21273
|
||||
.. _Pull Request 21286: https://github.com/galaxyproject/galaxy/pull/21286
|
||||
.. _Pull Request 21185: https://github.com/galaxyproject/galaxy/pull/21185
|
||||
.. _Pull Request 21184: https://github.com/galaxyproject/galaxy/pull/21184
|
||||
.. _Pull Request 21175: https://github.com/galaxyproject/galaxy/pull/21175
|
||||
.. _Pull Request 21181: https://github.com/galaxyproject/galaxy/pull/21181
|
||||
.. _Pull Request 21159: https://github.com/galaxyproject/galaxy/pull/21159
|
||||
.. _Pull Request 21166: https://github.com/galaxyproject/galaxy/pull/21166
|
||||
.. _Pull Request 21165: https://github.com/galaxyproject/galaxy/pull/21165
|
||||
.. _Pull Request 21164: https://github.com/galaxyproject/galaxy/pull/21164
|
||||
.. _Pull Request 21160: https://github.com/galaxyproject/galaxy/pull/21160
|
||||
.. _Pull Request 21169: https://github.com/galaxyproject/galaxy/pull/21169
|
||||
.. _Pull Request 21173: https://github.com/galaxyproject/galaxy/pull/21173
|
||||
.. _Pull Request 21085: https://github.com/galaxyproject/galaxy/pull/21085
|
||||
.. _Pull Request 21151: https://github.com/galaxyproject/galaxy/pull/21151
|
||||
.. _Pull Request 21156: https://github.com/galaxyproject/galaxy/pull/21156
|
||||
.. _Pull Request 20260: https://github.com/galaxyproject/galaxy/pull/20260
|
||||
.. _Pull Request 20268: https://github.com/galaxyproject/galaxy/pull/20268
|
||||
.. _Pull Request 20264: https://github.com/galaxyproject/galaxy/pull/20264
|
||||
.. _Pull Request 20278: https://github.com/galaxyproject/galaxy/pull/20278
|
||||
.. _Pull Request 20262: https://github.com/galaxyproject/galaxy/pull/20262
|
||||
.. _Pull Request 20284: https://github.com/galaxyproject/galaxy/pull/20284
|
||||
.. _Pull Request 20292: https://github.com/galaxyproject/galaxy/pull/20292
|
||||
.. _Pull Request 20291: https://github.com/galaxyproject/galaxy/pull/20291
|
||||
.. _Pull Request 20139: https://github.com/galaxyproject/galaxy/pull/20139
|
||||
.. _Pull Request 20347: https://github.com/galaxyproject/galaxy/pull/20347
|
||||
.. _Pull Request 20348: https://github.com/galaxyproject/galaxy/pull/20348
|
||||
.. _Pull Request 20355: https://github.com/galaxyproject/galaxy/pull/20355
|
||||
.. _Pull Request 20364: https://github.com/galaxyproject/galaxy/pull/20364
|
||||
.. _Pull Request 20408: https://github.com/galaxyproject/galaxy/pull/20408
|
||||
.. _Pull Request 20303: https://github.com/galaxyproject/galaxy/pull/20303
|
||||
.. _Pull Request 20422: https://github.com/galaxyproject/galaxy/pull/20422
|
||||
.. _Pull Request 20356: https://github.com/galaxyproject/galaxy/pull/20356
|
||||
.. _Pull Request 20357: https://github.com/galaxyproject/galaxy/pull/20357
|
||||
.. _Pull Request 20445: https://github.com/galaxyproject/galaxy/pull/20445
|
||||
.. _Pull Request 20446: https://github.com/galaxyproject/galaxy/pull/20446
|
||||
.. _Pull Request 20435: https://github.com/galaxyproject/galaxy/pull/20435
|
||||
.. _Pull Request 20387: https://github.com/galaxyproject/galaxy/pull/20387
|
||||
.. _Pull Request 20418: https://github.com/galaxyproject/galaxy/pull/20418
|
||||
.. _Pull Request 20383: https://github.com/galaxyproject/galaxy/pull/20383
|
||||
.. _Pull Request 20470: https://github.com/galaxyproject/galaxy/pull/20470
|
||||
.. _Pull Request 20372: https://github.com/galaxyproject/galaxy/pull/20372
|
||||
.. _Pull Request 20500: https://github.com/galaxyproject/galaxy/pull/20500
|
||||
.. _Pull Request 20501: https://github.com/galaxyproject/galaxy/pull/20501
|
||||
.. _Pull Request 20507: https://github.com/galaxyproject/galaxy/pull/20507
|
||||
.. _Pull Request 20509: https://github.com/galaxyproject/galaxy/pull/20509
|
||||
.. _Pull Request 20520: https://github.com/galaxyproject/galaxy/pull/20520
|
||||
.. _Pull Request 20516: https://github.com/galaxyproject/galaxy/pull/20516
|
||||
.. _Pull Request 20526: https://github.com/galaxyproject/galaxy/pull/20526
|
||||
.. _Pull Request 20527: https://github.com/galaxyproject/galaxy/pull/20527
|
||||
.. _Pull Request 20531: https://github.com/galaxyproject/galaxy/pull/20531
|
||||
.. _Pull Request 20529: https://github.com/galaxyproject/galaxy/pull/20529
|
||||
.. _Pull Request 20438: https://github.com/galaxyproject/galaxy/pull/20438
|
||||
.. _Pull Request 20511: https://github.com/galaxyproject/galaxy/pull/20511
|
||||
.. _Pull Request 20528: https://github.com/galaxyproject/galaxy/pull/20528
|
||||
.. _Pull Request 20518: https://github.com/galaxyproject/galaxy/pull/20518
|
||||
.. _Pull Request 20533: https://github.com/galaxyproject/galaxy/pull/20533
|
||||
.. _Pull Request 20534: https://github.com/galaxyproject/galaxy/pull/20534
|
||||
.. _Pull Request 20464: https://github.com/galaxyproject/galaxy/pull/20464
|
||||
.. _Pull Request 20536: https://github.com/galaxyproject/galaxy/pull/20536
|
||||
.. _Pull Request 20545: https://github.com/galaxyproject/galaxy/pull/20545
|
||||
.. _Pull Request 20354: https://github.com/galaxyproject/galaxy/pull/20354
|
||||
.. _Pull Request 20552: https://github.com/galaxyproject/galaxy/pull/20552
|
||||
.. _Pull Request 20525: https://github.com/galaxyproject/galaxy/pull/20525
|
||||
.. _Pull Request 20546: https://github.com/galaxyproject/galaxy/pull/20546
|
||||
.. _Pull Request 20537: https://github.com/galaxyproject/galaxy/pull/20537
|
||||
.. _Pull Request 20497: https://github.com/galaxyproject/galaxy/pull/20497
|
||||
.. _Pull Request 20577: https://github.com/galaxyproject/galaxy/pull/20577
|
||||
.. _Pull Request 20571: https://github.com/galaxyproject/galaxy/pull/20571
|
||||
.. _Pull Request 20584: https://github.com/galaxyproject/galaxy/pull/20584
|
||||
.. _Pull Request 20502: https://github.com/galaxyproject/galaxy/pull/20502
|
||||
.. _Pull Request 20591: https://github.com/galaxyproject/galaxy/pull/20591
|
||||
.. _Pull Request 20202: https://github.com/galaxyproject/galaxy/pull/20202
|
||||
.. _Pull Request 20593: https://github.com/galaxyproject/galaxy/pull/20593
|
||||
.. _Pull Request 20596: https://github.com/galaxyproject/galaxy/pull/20596
|
||||
.. _Pull Request 20601: https://github.com/galaxyproject/galaxy/pull/20601
|
||||
.. _Pull Request 20597: https://github.com/galaxyproject/galaxy/pull/20597
|
||||
.. _Pull Request 20594: https://github.com/galaxyproject/galaxy/pull/20594
|
||||
.. _Pull Request 20603: https://github.com/galaxyproject/galaxy/pull/20603
|
||||
.. _Pull Request 20460: https://github.com/galaxyproject/galaxy/pull/20460
|
||||
.. _Pull Request 20618: https://github.com/galaxyproject/galaxy/pull/20618
|
||||
.. _Pull Request 20521: https://github.com/galaxyproject/galaxy/pull/20521
|
||||
.. _Pull Request 20625: https://github.com/galaxyproject/galaxy/pull/20625
|
||||
.. _Pull Request 20615: https://github.com/galaxyproject/galaxy/pull/20615
|
||||
.. _Pull Request 20636: https://github.com/galaxyproject/galaxy/pull/20636
|
||||
.. _Pull Request 20632: https://github.com/galaxyproject/galaxy/pull/20632
|
||||
.. _Pull Request 20620: https://github.com/galaxyproject/galaxy/pull/20620
|
||||
.. _Pull Request 20639: https://github.com/galaxyproject/galaxy/pull/20639
|
||||
.. _Pull Request 20551: https://github.com/galaxyproject/galaxy/pull/20551
|
||||
.. _Pull Request 19697: https://github.com/galaxyproject/galaxy/pull/19697
|
||||
.. _Pull Request 20646: https://github.com/galaxyproject/galaxy/pull/20646
|
||||
.. _Pull Request 20638: https://github.com/galaxyproject/galaxy/pull/20638
|
||||
.. _Pull Request 20627: https://github.com/galaxyproject/galaxy/pull/20627
|
||||
.. _Pull Request 20651: https://github.com/galaxyproject/galaxy/pull/20651
|
||||
.. _Pull Request 20654: https://github.com/galaxyproject/galaxy/pull/20654
|
||||
.. _Pull Request 20649: https://github.com/galaxyproject/galaxy/pull/20649
|
||||
.. _Pull Request 20658: https://github.com/galaxyproject/galaxy/pull/20658
|
||||
.. _Pull Request 20652: https://github.com/galaxyproject/galaxy/pull/20652
|
||||
.. _Pull Request 20647: https://github.com/galaxyproject/galaxy/pull/20647
|
||||
.. _Pull Request 20653: https://github.com/galaxyproject/galaxy/pull/20653
|
||||
.. _Pull Request 20663: https://github.com/galaxyproject/galaxy/pull/20663
|
||||
.. _Pull Request 20665: https://github.com/galaxyproject/galaxy/pull/20665
|
||||
.. _Pull Request 20630: https://github.com/galaxyproject/galaxy/pull/20630
|
||||
.. _Pull Request 20664: https://github.com/galaxyproject/galaxy/pull/20664
|
||||
.. _Pull Request 20634: https://github.com/galaxyproject/galaxy/pull/20634
|
||||
.. _Pull Request 20669: https://github.com/galaxyproject/galaxy/pull/20669
|
||||
.. _Pull Request 20547: https://github.com/galaxyproject/galaxy/pull/20547
|
||||
.. _Pull Request 20672: https://github.com/galaxyproject/galaxy/pull/20672
|
||||
.. _Pull Request 20674: https://github.com/galaxyproject/galaxy/pull/20674
|
||||
.. _Pull Request 20496: https://github.com/galaxyproject/galaxy/pull/20496
|
||||
.. _Pull Request 20667: https://github.com/galaxyproject/galaxy/pull/20667
|
||||
.. _Pull Request 20680: https://github.com/galaxyproject/galaxy/pull/20680
|
||||
.. _Pull Request 20685: https://github.com/galaxyproject/galaxy/pull/20685
|
||||
.. _Pull Request 20690: https://github.com/galaxyproject/galaxy/pull/20690
|
||||
.. _Pull Request 20693: https://github.com/galaxyproject/galaxy/pull/20693
|
||||
.. _Pull Request 20696: https://github.com/galaxyproject/galaxy/pull/20696
|
||||
.. _Pull Request 20699: https://github.com/galaxyproject/galaxy/pull/20699
|
||||
.. _Pull Request 20694: https://github.com/galaxyproject/galaxy/pull/20694
|
||||
.. _Pull Request 20702: https://github.com/galaxyproject/galaxy/pull/20702
|
||||
.. _Pull Request 20586: https://github.com/galaxyproject/galaxy/pull/20586
|
||||
.. _Pull Request 20553: https://github.com/galaxyproject/galaxy/pull/20553
|
||||
.. _Pull Request 20703: https://github.com/galaxyproject/galaxy/pull/20703
|
||||
.. _Pull Request 20510: https://github.com/galaxyproject/galaxy/pull/20510
|
||||
.. _Pull Request 20684: https://github.com/galaxyproject/galaxy/pull/20684
|
||||
.. _Pull Request 20708: https://github.com/galaxyproject/galaxy/pull/20708
|
||||
.. _Pull Request 20522: https://github.com/galaxyproject/galaxy/pull/20522
|
||||
.. _Pull Request 20705: https://github.com/galaxyproject/galaxy/pull/20705
|
||||
.. _Pull Request 20729: https://github.com/galaxyproject/galaxy/pull/20729
|
||||
.. _Pull Request 20723: https://github.com/galaxyproject/galaxy/pull/20723
|
||||
.. _Pull Request 20721: https://github.com/galaxyproject/galaxy/pull/20721
|
||||
.. _Pull Request 20714: https://github.com/galaxyproject/galaxy/pull/20714
|
||||
.. _Pull Request 20732: https://github.com/galaxyproject/galaxy/pull/20732
|
||||
.. _Pull Request 20734: https://github.com/galaxyproject/galaxy/pull/20734
|
||||
.. _Pull Request 20727: https://github.com/galaxyproject/galaxy/pull/20727
|
||||
.. _Pull Request 20739: https://github.com/galaxyproject/galaxy/pull/20739
|
||||
.. _Pull Request 20753: https://github.com/galaxyproject/galaxy/pull/20753
|
||||
.. _Pull Request 20752: https://github.com/galaxyproject/galaxy/pull/20752
|
||||
.. _Pull Request 20755: https://github.com/galaxyproject/galaxy/pull/20755
|
||||
.. _Pull Request 20710: https://github.com/galaxyproject/galaxy/pull/20710
|
||||
.. _Pull Request 20760: https://github.com/galaxyproject/galaxy/pull/20760
|
||||
.. _Pull Request 20701: https://github.com/galaxyproject/galaxy/pull/20701
|
||||
.. _Pull Request 20736: https://github.com/galaxyproject/galaxy/pull/20736
|
||||
.. _Pull Request 20731: https://github.com/galaxyproject/galaxy/pull/20731
|
||||
.. _Pull Request 20762: https://github.com/galaxyproject/galaxy/pull/20762
|
||||
.. _Pull Request 20772: https://github.com/galaxyproject/galaxy/pull/20772
|
||||
.. _Pull Request 20769: https://github.com/galaxyproject/galaxy/pull/20769
|
||||
.. _Pull Request 20770: https://github.com/galaxyproject/galaxy/pull/20770
|
||||
.. _Pull Request 20775: https://github.com/galaxyproject/galaxy/pull/20775
|
||||
.. _Pull Request 20768: https://github.com/galaxyproject/galaxy/pull/20768
|
||||
.. _Pull Request 20779: https://github.com/galaxyproject/galaxy/pull/20779
|
||||
.. _Pull Request 20777: https://github.com/galaxyproject/galaxy/pull/20777
|
||||
.. _Pull Request 20749: https://github.com/galaxyproject/galaxy/pull/20749
|
||||
.. _Pull Request 20384: https://github.com/galaxyproject/galaxy/pull/20384
|
||||
.. _Pull Request 20402: https://github.com/galaxyproject/galaxy/pull/20402
|
||||
.. _Pull Request 20782: https://github.com/galaxyproject/galaxy/pull/20782
|
||||
.. _Pull Request 20784: https://github.com/galaxyproject/galaxy/pull/20784
|
||||
.. _Pull Request 20728: https://github.com/galaxyproject/galaxy/pull/20728
|
||||
.. _Pull Request 20698: https://github.com/galaxyproject/galaxy/pull/20698
|
||||
.. _Pull Request 20783: https://github.com/galaxyproject/galaxy/pull/20783
|
||||
.. _Pull Request 20795: https://github.com/galaxyproject/galaxy/pull/20795
|
||||
.. _Pull Request 20786: https://github.com/galaxyproject/galaxy/pull/20786
|
||||
.. _Pull Request 20806: https://github.com/galaxyproject/galaxy/pull/20806
|
||||
.. _Pull Request 20812: https://github.com/galaxyproject/galaxy/pull/20812
|
||||
.. _Pull Request 20807: https://github.com/galaxyproject/galaxy/pull/20807
|
||||
.. _Pull Request 20813: https://github.com/galaxyproject/galaxy/pull/20813
|
||||
.. _Pull Request 20814: https://github.com/galaxyproject/galaxy/pull/20814
|
||||
.. _Pull Request 20799: https://github.com/galaxyproject/galaxy/pull/20799
|
||||
.. _Pull Request 20794: https://github.com/galaxyproject/galaxy/pull/20794
|
||||
.. _Pull Request 20800: https://github.com/galaxyproject/galaxy/pull/20800
|
||||
.. _Pull Request 20774: https://github.com/galaxyproject/galaxy/pull/20774
|
||||
.. _Pull Request 20822: https://github.com/galaxyproject/galaxy/pull/20822
|
||||
.. _Pull Request 20771: https://github.com/galaxyproject/galaxy/pull/20771
|
||||
.. _Pull Request 20823: https://github.com/galaxyproject/galaxy/pull/20823
|
||||
.. _Pull Request 20824: https://github.com/galaxyproject/galaxy/pull/20824
|
||||
.. _Pull Request 20829: https://github.com/galaxyproject/galaxy/pull/20829
|
||||
.. _Pull Request 20834: https://github.com/galaxyproject/galaxy/pull/20834
|
||||
.. _Pull Request 20797: https://github.com/galaxyproject/galaxy/pull/20797
|
||||
.. _Pull Request 20836: https://github.com/galaxyproject/galaxy/pull/20836
|
||||
.. _Pull Request 20837: https://github.com/galaxyproject/galaxy/pull/20837
|
||||
.. _Pull Request 20841: https://github.com/galaxyproject/galaxy/pull/20841
|
||||
.. _Pull Request 20761: https://github.com/galaxyproject/galaxy/pull/20761
|
||||
.. _Pull Request 20854: https://github.com/galaxyproject/galaxy/pull/20854
|
||||
.. _Pull Request 20866: https://github.com/galaxyproject/galaxy/pull/20866
|
||||
.. _Pull Request 20811: https://github.com/galaxyproject/galaxy/pull/20811
|
||||
.. _Pull Request 20869: https://github.com/galaxyproject/galaxy/pull/20869
|
||||
.. _Pull Request 20863: https://github.com/galaxyproject/galaxy/pull/20863
|
||||
.. _Pull Request 20871: https://github.com/galaxyproject/galaxy/pull/20871
|
||||
.. _Pull Request 20873: https://github.com/galaxyproject/galaxy/pull/20873
|
||||
.. _Pull Request 20853: https://github.com/galaxyproject/galaxy/pull/20853
|
||||
.. _Pull Request 20859: https://github.com/galaxyproject/galaxy/pull/20859
|
||||
.. _Pull Request 20872: https://github.com/galaxyproject/galaxy/pull/20872
|
||||
.. _Pull Request 20870: https://github.com/galaxyproject/galaxy/pull/20870
|
||||
.. _Pull Request 20877: https://github.com/galaxyproject/galaxy/pull/20877
|
||||
.. _Pull Request 20875: https://github.com/galaxyproject/galaxy/pull/20875
|
||||
.. _Pull Request 20874: https://github.com/galaxyproject/galaxy/pull/20874
|
||||
.. _Pull Request 20884: https://github.com/galaxyproject/galaxy/pull/20884
|
||||
.. _Pull Request 20889: https://github.com/galaxyproject/galaxy/pull/20889
|
||||
.. _Pull Request 20888: https://github.com/galaxyproject/galaxy/pull/20888
|
||||
.. _Pull Request 20886: https://github.com/galaxyproject/galaxy/pull/20886
|
||||
.. _Pull Request 20891: https://github.com/galaxyproject/galaxy/pull/20891
|
||||
.. _Pull Request 20876: https://github.com/galaxyproject/galaxy/pull/20876
|
||||
.. _Pull Request 20892: https://github.com/galaxyproject/galaxy/pull/20892
|
||||
.. _Pull Request 20887: https://github.com/galaxyproject/galaxy/pull/20887
|
||||
.. _Pull Request 20890: https://github.com/galaxyproject/galaxy/pull/20890
|
||||
.. _Pull Request 20880: https://github.com/galaxyproject/galaxy/pull/20880
|
||||
.. _Pull Request 20893: https://github.com/galaxyproject/galaxy/pull/20893
|
||||
.. _Pull Request 20895: https://github.com/galaxyproject/galaxy/pull/20895
|
||||
.. _Pull Request 20827: https://github.com/galaxyproject/galaxy/pull/20827
|
||||
.. _Pull Request 20905: https://github.com/galaxyproject/galaxy/pull/20905
|
||||
.. _Pull Request 20862: https://github.com/galaxyproject/galaxy/pull/20862
|
||||
.. _Pull Request 20908: https://github.com/galaxyproject/galaxy/pull/20908
|
||||
.. _Pull Request 20907: https://github.com/galaxyproject/galaxy/pull/20907
|
||||
.. _Pull Request 20778: https://github.com/galaxyproject/galaxy/pull/20778
|
||||
.. _Pull Request 20332: https://github.com/galaxyproject/galaxy/pull/20332
|
||||
.. _Pull Request 20909: https://github.com/galaxyproject/galaxy/pull/20909
|
||||
.. _Pull Request 20650: https://github.com/galaxyproject/galaxy/pull/20650
|
||||
.. _Pull Request 20915: https://github.com/galaxyproject/galaxy/pull/20915
|
||||
.. _Pull Request 20920: https://github.com/galaxyproject/galaxy/pull/20920
|
||||
.. _Pull Request 20918: https://github.com/galaxyproject/galaxy/pull/20918
|
||||
.. _Pull Request 20919: https://github.com/galaxyproject/galaxy/pull/20919
|
||||
.. _Pull Request 20922: https://github.com/galaxyproject/galaxy/pull/20922
|
||||
.. _Pull Request 20921: https://github.com/galaxyproject/galaxy/pull/20921
|
||||
.. _Pull Request 20917: https://github.com/galaxyproject/galaxy/pull/20917
|
||||
.. _Pull Request 20925: https://github.com/galaxyproject/galaxy/pull/20925
|
||||
.. _Pull Request 20930: https://github.com/galaxyproject/galaxy/pull/20930
|
||||
.. _Pull Request 20928: https://github.com/galaxyproject/galaxy/pull/20928
|
||||
.. _Pull Request 20932: https://github.com/galaxyproject/galaxy/pull/20932
|
||||
.. _Pull Request 20941: https://github.com/galaxyproject/galaxy/pull/20941
|
||||
.. _Pull Request 20939: https://github.com/galaxyproject/galaxy/pull/20939
|
||||
.. _Pull Request 20938: https://github.com/galaxyproject/galaxy/pull/20938
|
||||
.. _Pull Request 20937: https://github.com/galaxyproject/galaxy/pull/20937
|
||||
.. _Pull Request 20942: https://github.com/galaxyproject/galaxy/pull/20942
|
||||
.. _Pull Request 19086: https://github.com/galaxyproject/galaxy/pull/19086
|
||||
.. _Pull Request 20838: https://github.com/galaxyproject/galaxy/pull/20838
|
||||
.. _Pull Request 20361: https://github.com/galaxyproject/galaxy/pull/20361
|
||||
.. _Pull Request 20940: https://github.com/galaxyproject/galaxy/pull/20940
|
||||
.. _Pull Request 18732: https://github.com/galaxyproject/galaxy/pull/18732
|
||||
.. _Pull Request 20899: https://github.com/galaxyproject/galaxy/pull/20899
|
||||
.. _Pull Request 20717: https://github.com/galaxyproject/galaxy/pull/20717
|
||||
.. _Pull Request 20946: https://github.com/galaxyproject/galaxy/pull/20946
|
||||
.. _Pull Request 20951: https://github.com/galaxyproject/galaxy/pull/20951
|
||||
.. _Pull Request 20851: https://github.com/galaxyproject/galaxy/pull/20851
|
||||
.. _Pull Request 20945: https://github.com/galaxyproject/galaxy/pull/20945
|
||||
.. _Pull Request 20865: https://github.com/galaxyproject/galaxy/pull/20865
|
||||
.. _Pull Request 20957: https://github.com/galaxyproject/galaxy/pull/20957
|
||||
.. _Pull Request 20962: https://github.com/galaxyproject/galaxy/pull/20962
|
||||
.. _Pull Request 20965: https://github.com/galaxyproject/galaxy/pull/20965
|
||||
.. _Pull Request 20718: https://github.com/galaxyproject/galaxy/pull/20718
|
||||
.. _Pull Request 20963: https://github.com/galaxyproject/galaxy/pull/20963
|
||||
.. _Pull Request 20975: https://github.com/galaxyproject/galaxy/pull/20975
|
||||
.. _Pull Request 20949: https://github.com/galaxyproject/galaxy/pull/20949
|
||||
.. _Pull Request 20954: https://github.com/galaxyproject/galaxy/pull/20954
|
||||
.. _Pull Request 20906: https://github.com/galaxyproject/galaxy/pull/20906
|
||||
.. _Pull Request 20885: https://github.com/galaxyproject/galaxy/pull/20885
|
||||
.. _Pull Request 20707: https://github.com/galaxyproject/galaxy/pull/20707
|
||||
.. _Pull Request 20828: https://github.com/galaxyproject/galaxy/pull/20828
|
||||
.. _Pull Request 20931: https://github.com/galaxyproject/galaxy/pull/20931
|
||||
.. _Pull Request 20960: https://github.com/galaxyproject/galaxy/pull/20960
|
||||
.. _Pull Request 20980: https://github.com/galaxyproject/galaxy/pull/20980
|
||||
.. _Pull Request 20926: https://github.com/galaxyproject/galaxy/pull/20926
|
||||
.. _Pull Request 20916: https://github.com/galaxyproject/galaxy/pull/20916
|
||||
.. _Pull Request 20840: https://github.com/galaxyproject/galaxy/pull/20840
|
||||
.. _Pull Request 20830: https://github.com/galaxyproject/galaxy/pull/20830
|
||||
.. _Pull Request 20820: https://github.com/galaxyproject/galaxy/pull/20820
|
||||
.. _Pull Request 20177: https://github.com/galaxyproject/galaxy/pull/20177
|
||||
.. _Pull Request 19817: https://github.com/galaxyproject/galaxy/pull/19817
|
||||
.. _Pull Request 20929: https://github.com/galaxyproject/galaxy/pull/20929
|
||||
.. _Pull Request 20466: https://github.com/galaxyproject/galaxy/pull/20466
|
||||
.. _Pull Request 20692: https://github.com/galaxyproject/galaxy/pull/20692
|
||||
.. _Pull Request 20986: https://github.com/galaxyproject/galaxy/pull/20986
|
||||
.. _Pull Request 13570: https://github.com/galaxyproject/galaxy/pull/13570
|
||||
.. _Pull Request 20519: https://github.com/galaxyproject/galaxy/pull/20519
|
||||
.. _Pull Request 20523: https://github.com/galaxyproject/galaxy/pull/20523
|
||||
.. _Pull Request 20524: https://github.com/galaxyproject/galaxy/pull/20524
|
||||
.. _Pull Request 20542: https://github.com/galaxyproject/galaxy/pull/20542
|
||||
.. _Pull Request 20566: https://github.com/galaxyproject/galaxy/pull/20566
|
||||
.. _Pull Request 20575: https://github.com/galaxyproject/galaxy/pull/20575
|
||||
.. _Pull Request 20582: https://github.com/galaxyproject/galaxy/pull/20582
|
||||
.. _Pull Request 20599: https://github.com/galaxyproject/galaxy/pull/20599
|
||||
.. _Pull Request 20656: https://github.com/galaxyproject/galaxy/pull/20656
|
||||
.. _Pull Request 20676: https://github.com/galaxyproject/galaxy/pull/20676
|
||||
.. _Pull Request 20713: https://github.com/galaxyproject/galaxy/pull/20713
|
||||
.. _Pull Request 20780: https://github.com/galaxyproject/galaxy/pull/20780
|
||||
.. _Pull Request 20856: https://github.com/galaxyproject/galaxy/pull/20856
|
||||
.. _Pull Request 20883: https://github.com/galaxyproject/galaxy/pull/20883
|
||||
.. _Pull Request 20936: https://github.com/galaxyproject/galaxy/pull/20936
|
||||
.. _Pull Request 20953: https://github.com/galaxyproject/galaxy/pull/20953
|
||||
.. _Pull Request 20968: https://github.com/galaxyproject/galaxy/pull/20968
|
||||
.. _Pull Request 20970: https://github.com/galaxyproject/galaxy/pull/20970
|
||||
.. _Pull Request 20976: https://github.com/galaxyproject/galaxy/pull/20976
|
||||
.. _Pull Request 20982: https://github.com/galaxyproject/galaxy/pull/20982
|
||||
.. _Pull Request 20983: https://github.com/galaxyproject/galaxy/pull/20983
|
||||
.. _Pull Request 20984: https://github.com/galaxyproject/galaxy/pull/20984
|
||||
.. _Pull Request 20844: https://github.com/galaxyproject/galaxy/pull/20844
|
||||
.. _Pull Request 20994: https://github.com/galaxyproject/galaxy/pull/20994
|
||||
.. _Pull Request 20971: https://github.com/galaxyproject/galaxy/pull/20971
|
||||
.. _Pull Request 20662: https://github.com/galaxyproject/galaxy/pull/20662
|
||||
.. _Pull Request 20576: https://github.com/galaxyproject/galaxy/pull/20576
|
||||
.. _Pull Request 20626: https://github.com/galaxyproject/galaxy/pull/20626
|
||||
.. _Pull Request 20815: https://github.com/galaxyproject/galaxy/pull/20815
|
||||
.. _Pull Request 20845: https://github.com/galaxyproject/galaxy/pull/20845
|
||||
.. _Pull Request 20992: https://github.com/galaxyproject/galaxy/pull/20992
|
||||
.. _Pull Request 20826: https://github.com/galaxyproject/galaxy/pull/20826
|
||||
.. _Pull Request 20642: https://github.com/galaxyproject/galaxy/pull/20642
|
||||
.. _Pull Request 20788: https://github.com/galaxyproject/galaxy/pull/20788
|
||||
.. _Pull Request 20996: https://github.com/galaxyproject/galaxy/pull/20996
|
||||
.. _Pull Request 21003: https://github.com/galaxyproject/galaxy/pull/21003
|
||||
.. _Pull Request 20999: https://github.com/galaxyproject/galaxy/pull/20999
|
||||
.. _Pull Request 21006: https://github.com/galaxyproject/galaxy/pull/21006
|
||||
.. _Pull Request 21007: https://github.com/galaxyproject/galaxy/pull/21007
|
||||
.. _Pull Request 20985: https://github.com/galaxyproject/galaxy/pull/20985
|
||||
.. _Pull Request 21005: https://github.com/galaxyproject/galaxy/pull/21005
|
||||
.. _Pull Request 20754: https://github.com/galaxyproject/galaxy/pull/20754
|
||||
.. _Pull Request 21009: https://github.com/galaxyproject/galaxy/pull/21009
|
||||
.. _Pull Request 21012: https://github.com/galaxyproject/galaxy/pull/21012
|
||||
.. _Pull Request 21014: https://github.com/galaxyproject/galaxy/pull/21014
|
||||
.. _Pull Request 21017: https://github.com/galaxyproject/galaxy/pull/21017
|
||||
.. _Pull Request 21020: https://github.com/galaxyproject/galaxy/pull/21020
|
||||
.. _Pull Request 21018: https://github.com/galaxyproject/galaxy/pull/21018
|
||||
.. _Pull Request 21019: https://github.com/galaxyproject/galaxy/pull/21019
|
||||
.. _Pull Request 21022: https://github.com/galaxyproject/galaxy/pull/21022
|
||||
.. _Pull Request 21026: https://github.com/galaxyproject/galaxy/pull/21026
|
||||
.. _Pull Request 21045: https://github.com/galaxyproject/galaxy/pull/21045
|
||||
.. _Pull Request 20801: https://github.com/galaxyproject/galaxy/pull/20801
|
||||
.. _Pull Request 20757: https://github.com/galaxyproject/galaxy/pull/20757
|
||||
.. _Pull Request 20898: https://github.com/galaxyproject/galaxy/pull/20898
|
||||
.. _Pull Request 20987: https://github.com/galaxyproject/galaxy/pull/20987
|
||||
.. _Pull Request 21056: https://github.com/galaxyproject/galaxy/pull/21056
|
||||
.. _Pull Request 21055: https://github.com/galaxyproject/galaxy/pull/21055
|
||||
.. _Pull Request 21070: https://github.com/galaxyproject/galaxy/pull/21070
|
||||
.. _Pull Request 21081: https://github.com/galaxyproject/galaxy/pull/21081
|
||||
.. _Pull Request 21095: https://github.com/galaxyproject/galaxy/pull/21095
|
||||
.. _Pull Request 20821: https://github.com/galaxyproject/galaxy/pull/20821
|
||||
.. _Pull Request 21072: https://github.com/galaxyproject/galaxy/pull/21072
|
||||
.. _Pull Request 21094: https://github.com/galaxyproject/galaxy/pull/21094
|
||||
.. _Pull Request 21087: https://github.com/galaxyproject/galaxy/pull/21087
|
||||
.. _Pull Request 21091: https://github.com/galaxyproject/galaxy/pull/21091
|
||||
.. _Pull Request 21096: https://github.com/galaxyproject/galaxy/pull/21096
|
||||
.. _Pull Request 21035: https://github.com/galaxyproject/galaxy/pull/21035
|
||||
.. _Pull Request 21105: https://github.com/galaxyproject/galaxy/pull/21105
|
||||
.. _Pull Request 21112: https://github.com/galaxyproject/galaxy/pull/21112
|
||||
.. _Pull Request 21117: https://github.com/galaxyproject/galaxy/pull/21117
|
||||
.. _Pull Request 21115: https://github.com/galaxyproject/galaxy/pull/21115
|
||||
.. _Pull Request 21049: https://github.com/galaxyproject/galaxy/pull/21049
|
||||
.. _Pull Request 21060: https://github.com/galaxyproject/galaxy/pull/21060
|
||||
.. _Pull Request 21078: https://github.com/galaxyproject/galaxy/pull/21078
|
||||
.. _Pull Request 20424: https://github.com/galaxyproject/galaxy/pull/20424
|
||||
.. _Pull Request 21107: https://github.com/galaxyproject/galaxy/pull/21107
|
||||
.. _Pull Request 20427: https://github.com/galaxyproject/galaxy/pull/20427
|
||||
.. _Pull Request 20550: https://github.com/galaxyproject/galaxy/pull/20550
|
||||
.. _Pull Request 20558: https://github.com/galaxyproject/galaxy/pull/20558
|
||||
.. _Pull Request 20565: https://github.com/galaxyproject/galaxy/pull/20565
|
||||
.. _Pull Request 20585: https://github.com/galaxyproject/galaxy/pull/20585
|
||||
.. _Pull Request 20592: https://github.com/galaxyproject/galaxy/pull/20592
|
||||
.. _Pull Request 20609: https://github.com/galaxyproject/galaxy/pull/20609
|
||||
.. _Pull Request 20624: https://github.com/galaxyproject/galaxy/pull/20624
|
||||
.. _Pull Request 20666: https://github.com/galaxyproject/galaxy/pull/20666
|
||||
.. _Pull Request 20719: https://github.com/galaxyproject/galaxy/pull/20719
|
||||
.. _Pull Request 20737: https://github.com/galaxyproject/galaxy/pull/20737
|
||||
.. _Pull Request 20738: https://github.com/galaxyproject/galaxy/pull/20738
|
||||
.. _Pull Request 20744: https://github.com/galaxyproject/galaxy/pull/20744
|
||||
.. _Pull Request 20747: https://github.com/galaxyproject/galaxy/pull/20747
|
||||
.. _Pull Request 20776: https://github.com/galaxyproject/galaxy/pull/20776
|
||||
.. _Pull Request 20798: https://github.com/galaxyproject/galaxy/pull/20798
|
||||
.. _Pull Request 20805: https://github.com/galaxyproject/galaxy/pull/20805
|
||||
.. _Pull Request 20839: https://github.com/galaxyproject/galaxy/pull/20839
|
||||
.. _Pull Request 20868: https://github.com/galaxyproject/galaxy/pull/20868
|
||||
.. _Pull Request 20881: https://github.com/galaxyproject/galaxy/pull/20881
|
||||
.. _Pull Request 20912: https://github.com/galaxyproject/galaxy/pull/20912
|
||||
.. _Pull Request 20914: https://github.com/galaxyproject/galaxy/pull/20914
|
||||
.. _Pull Request 20943: https://github.com/galaxyproject/galaxy/pull/20943
|
||||
.. _Pull Request 20947: https://github.com/galaxyproject/galaxy/pull/20947
|
||||
.. _Pull Request 21025: https://github.com/galaxyproject/galaxy/pull/21025
|
||||
.. _Pull Request 19084: https://github.com/galaxyproject/galaxy/pull/19084
|
||||
.. _Pull Request 19225: https://github.com/galaxyproject/galaxy/pull/19225
|
||||
.. _Pull Request 19305: https://github.com/galaxyproject/galaxy/pull/19305
|
||||
.. _Pull Request 19318: https://github.com/galaxyproject/galaxy/pull/19318
|
||||
.. _Pull Request 19658: https://github.com/galaxyproject/galaxy/pull/19658
|
||||
.. _Pull Request 19973: https://github.com/galaxyproject/galaxy/pull/19973
|
||||
.. _Pull Request 20287: https://github.com/galaxyproject/galaxy/pull/20287
|
||||
.. _Pull Request 20288: https://github.com/galaxyproject/galaxy/pull/20288
|
||||
.. _Pull Request 20390: https://github.com/galaxyproject/galaxy/pull/20390
|
||||
.. _Pull Request 21051: https://github.com/galaxyproject/galaxy/pull/21051
|
||||
.. _Pull Request 21021: https://github.com/galaxyproject/galaxy/pull/21021
|
||||
.. _Pull Request 21130: https://github.com/galaxyproject/galaxy/pull/21130
|
||||
.. _Pull Request 21134: https://github.com/galaxyproject/galaxy/pull/21134
|
||||
.. _Pull Request 21138: https://github.com/galaxyproject/galaxy/pull/21138
|
||||
.. _Pull Request 20539: https://github.com/galaxyproject/galaxy/pull/20539
|
||||
.. _Pull Request 20629: https://github.com/galaxyproject/galaxy/pull/20629
|
||||
.. _Pull Request 21141: https://github.com/galaxyproject/galaxy/pull/21141
|
||||
.. _Pull Request 21145: https://github.com/galaxyproject/galaxy/pull/21145
|
||||
.. _Pull Request 21142: https://github.com/galaxyproject/galaxy/pull/21142
|
||||
.. _Pull Request 21140: https://github.com/galaxyproject/galaxy/pull/21140
|
||||
.. _Pull Request 21149: https://github.com/galaxyproject/galaxy/pull/21149
|
||||
@@ -0,0 +1,6 @@
|
||||
|
||||
:orphan:
|
||||
|
||||
===========================================================
|
||||
26.0 Galaxy Release
|
||||
===========================================================
|
||||
@@ -4,6 +4,7 @@ Releases
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
||||
25.1_announce_user
|
||||
25.0_announce_user
|
||||
24.2_announce_user
|
||||
24.1_announce_user
|
||||
|
||||
@@ -158,11 +158,17 @@ class DatasetCollectionManager:
|
||||
substructure, allow_uninitialized_element=allow_uninitialized_element
|
||||
)
|
||||
|
||||
# Preserve columns metadata from input structure for sample sheets
|
||||
columns = None
|
||||
if structure.columns_metadata and identifier in structure.columns_metadata:
|
||||
columns = structure.columns_metadata[identifier]
|
||||
|
||||
element = model.DatasetCollectionElement(
|
||||
collection=dataset_collection,
|
||||
element=element,
|
||||
element_identifier=identifier,
|
||||
element_index=index,
|
||||
columns=columns,
|
||||
)
|
||||
elements.append(element)
|
||||
dataset_collection.element_count = len(elements)
|
||||
|
||||
@@ -7378,7 +7378,11 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
|
||||
minimize_copies=False,
|
||||
copy_hid=True,
|
||||
):
|
||||
new_collection = DatasetCollection(collection_type=self.collection_type, element_count=self.element_count)
|
||||
new_collection = DatasetCollection(
|
||||
collection_type=self.collection_type,
|
||||
element_count=self.element_count,
|
||||
column_definitions=self.column_definitions,
|
||||
)
|
||||
for element in self.elements:
|
||||
element.copy_to_collection(
|
||||
new_collection,
|
||||
|
||||
@@ -96,9 +96,10 @@ class DatabaseHeartbeat:
|
||||
session.add(worker_process)
|
||||
# We only want a single process watching the various config files on the file system.
|
||||
# We just pick the max server name for simplicity
|
||||
is_config_watcher = self.server_name == max(
|
||||
webapp_servers = [
|
||||
p.server_name for p in self.get_active_processes(self.heartbeat_interval + 1) if p.app_type == WEBAPP
|
||||
)
|
||||
]
|
||||
is_config_watcher = bool(webapp_servers) and self.server_name == max(webapp_servers)
|
||||
if is_config_watcher != self.is_config_watcher:
|
||||
self.is_config_watcher = is_config_watcher
|
||||
|
||||
|
||||
@@ -64,14 +64,17 @@ class UninitializedTree(BaseTree):
|
||||
class Tree(BaseTree):
|
||||
children_known = True
|
||||
|
||||
def __init__(self, children, collection_type_description, when_values=None):
|
||||
def __init__(self, children, collection_type_description, when_values=None, columns_metadata=None):
|
||||
super().__init__(collection_type_description)
|
||||
self.children = children
|
||||
self.when_values = when_values
|
||||
# columns_metadata is a dict mapping element_identifier to columns data
|
||||
self.columns_metadata = columns_metadata or {}
|
||||
|
||||
@staticmethod
|
||||
def for_dataset_collection(dataset_collection, collection_type_description):
|
||||
children = []
|
||||
columns_metadata = {}
|
||||
for element in dataset_collection.elements:
|
||||
if collection_type_description.has_subcollections():
|
||||
child_collection = element.child_collection
|
||||
@@ -84,7 +87,10 @@ class Tree(BaseTree):
|
||||
children.append((element.element_identifier, tree))
|
||||
else:
|
||||
children.append((element.element_identifier, leaf))
|
||||
return Tree(children, collection_type_description)
|
||||
# Capture columns metadata from sample sheet collections
|
||||
if element.columns is not None:
|
||||
columns_metadata[element.element_identifier] = element.columns
|
||||
return Tree(children, collection_type_description, columns_metadata=columns_metadata)
|
||||
|
||||
def walk_collections(self, hdca_dict):
|
||||
return self._walk_collections(dict_map(lambda hdca: hdca.collection, hdca_dict))
|
||||
@@ -142,11 +148,12 @@ class Tree(BaseTree):
|
||||
for identifier, structure in self.children:
|
||||
new_children.append((identifier, structure.multiply(other_structure)))
|
||||
|
||||
return Tree(new_children, new_collection_type)
|
||||
# Preserve columns_metadata when multiplying
|
||||
return Tree(new_children, new_collection_type, columns_metadata=self.columns_metadata.copy())
|
||||
|
||||
def clone(self):
|
||||
cloned_children = [(_[0], _[1].clone()) for _ in self.children]
|
||||
return Tree(cloned_children, self.collection_type_description)
|
||||
return Tree(cloned_children, self.collection_type_description, columns_metadata=self.columns_metadata.copy())
|
||||
|
||||
def __str__(self):
|
||||
return f"Tree[collection_type={self.collection_type_description},children=({','.join(f'{identifier_and_element[0]}={identifier_and_element[1]}' for identifier_and_element in self.children)})]"
|
||||
|
||||
@@ -14,5 +14,5 @@ REVISION_TAGS = {
|
||||
"24.1": "04288b6a5b25",
|
||||
"24.2": "a4c3ef999ab5",
|
||||
"25.0": "c716ee82337b",
|
||||
"25.1": "cd26484899fb",
|
||||
"25.1": "63dc6cca023f",
|
||||
}
|
||||
|
||||
@@ -6,7 +6,13 @@
|
||||
<edam_operation>operation_3359</edam_operation>
|
||||
</edam_operations>
|
||||
<configfiles>
|
||||
<configfile name="out_config"><![CDATA[#for $key in $input.keys()
|
||||
<configfile name="out_config"><![CDATA[#if $include_headers and $input.collection.column_definitions
|
||||
#set $headers = [col_def['name'] for col_def in $input.collection.column_definitions]
|
||||
#set $header_string = '\t'.join($headers)
|
||||
#set $tab = '\t'
|
||||
element_identifier$tab$header_string
|
||||
#end if
|
||||
#for $key in $input.keys()
|
||||
#set $row = $input.sample_sheet_row($key)
|
||||
#set $row_as_string = '\t'.join(map(lambda x: str($none_replace) if x is None else (str($empty_replace) if x == "" else (str($bool_true_replace) if x is True else (str($bool_false_replace) if x is False else str(x)))), $row))
|
||||
#set $tab = '\t'
|
||||
@@ -19,6 +25,8 @@ cp '$out_config' '$output'
|
||||
|
||||
<inputs>
|
||||
<param type="data_collection" collection_type="sample_sheet,sample_sheet:paired,sample_sheet:paired_or_unpaired,sample_sheet:record" name="input" label="Sample sheet to convert" />
|
||||
<param name="include_headers" label="Include column headers" type="boolean" checked="false" help="If enabled, the first line of output will contain the column names from the sample sheet definition.">
|
||||
</param>
|
||||
<param name="none_replace" label="Replace 'null' values with" type="text" value="" help="Default is just an empty string '', but in some cases '-' might read better.">
|
||||
</param>
|
||||
<param name="empty_replace" label="Replace empty string values with" type="text" value="" help="Default is just to keep the empty string '', but in some cases '-' might read better.">
|
||||
@@ -39,5 +47,11 @@ Synopsis
|
||||
|
||||
Takes a sample sheet dataset collection and converts the sample sheet metadata into a tabular dataset.
|
||||
|
||||
The output is a tab-separated file where each row corresponds to an element in the sample sheet collection.
|
||||
The first column contains the element identifier, followed by columns for each metadata field defined in the sample sheet.
|
||||
|
||||
When "Include column headers" is enabled, the first row will contain the column names, with "element_identifier"
|
||||
as the first column followed by the names from the sample sheet column definitions.
|
||||
|
||||
]]></help>
|
||||
</tool>
|
||||
|
||||
+70
-10
@@ -224,6 +224,12 @@ class WorkflowInvoker:
|
||||
remaining_steps = self.progress.remaining_steps()
|
||||
delayed_steps = False
|
||||
max_jobs_per_iteration_reached = False
|
||||
|
||||
# Pre-populate outputs for all input steps so subworkflows can access them
|
||||
for step in self.workflow_invocation.workflow.steps:
|
||||
if step.is_input_type:
|
||||
self.progress._ensure_input_step_outputs_populated(step)
|
||||
|
||||
for step, workflow_invocation_step in remaining_steps:
|
||||
max_jobs_to_schedule = self.progress.maximum_jobs_to_schedule_or_none
|
||||
if max_jobs_to_schedule is not None and max_jobs_to_schedule <= 0:
|
||||
@@ -255,13 +261,29 @@ class WorkflowInvoker:
|
||||
self.progress.mark_step_outputs_delayed(step, why=de.why)
|
||||
except Exception as e:
|
||||
log_function = log.error
|
||||
if isinstance(e, modules.FailWorkflowEvaluation) and e.why.reason in FAILURE_REASONS_EXPECTED:
|
||||
log_function = log.info
|
||||
failure_details = []
|
||||
if isinstance(e, modules.FailWorkflowEvaluation):
|
||||
if e.why.reason in FAILURE_REASONS_EXPECTED:
|
||||
log_function = log.info
|
||||
failure_details.append(f"reason={e.why.reason}")
|
||||
if hasattr(e.why, "output_name") and e.why.output_name:
|
||||
failure_details.append(f"output_name={e.why.output_name}")
|
||||
if hasattr(e.why, "dependent_workflow_step_id") and e.why.dependent_workflow_step_id:
|
||||
failure_details.append(f"dependent_step_id={e.why.dependent_workflow_step_id}")
|
||||
if hasattr(e.why, "workflow_step_id") and e.why.workflow_step_id:
|
||||
failure_details.append(f"failed_step_id={e.why.workflow_step_id}")
|
||||
if hasattr(e.why, "details") and e.why.details:
|
||||
failure_details.append(f"details={e.why.details}")
|
||||
else:
|
||||
failure_details.append(f"{type(e).__name__}: {str(e)}")
|
||||
failure_reason = ", ".join(failure_details) if failure_details else "unknown"
|
||||
|
||||
log_function(
|
||||
"Failed to schedule %s for %s, problem occurred on %s.",
|
||||
"Failed to schedule %s for %s, problem occurred on %s. Failure reason: %s",
|
||||
self.workflow_invocation.log_str(),
|
||||
self.workflow_invocation.workflow.log_str(),
|
||||
step.log_str(),
|
||||
failure_reason,
|
||||
)
|
||||
if isinstance(e, MessageException):
|
||||
# This is the highest level at which we can inject the step id
|
||||
@@ -578,14 +600,26 @@ class WorkflowProgress:
|
||||
if outputs is None:
|
||||
outputs = {}
|
||||
|
||||
if self.inputs_by_step_id:
|
||||
step_id = step.id
|
||||
if step_id not in self.inputs_by_step_id and "output" not in outputs:
|
||||
default_value = step.get_input_default_value(NO_REPLACEMENT)
|
||||
outputs["output"] = default_value
|
||||
elif step_id in self.inputs_by_step_id:
|
||||
if self.inputs_by_step_id[step_id] is not None or "output" not in outputs:
|
||||
# Check if we have a pre-populated value from _ensure_input_step_outputs_populated
|
||||
# This takes precedence over values from step.state.inputs for input steps
|
||||
# Only use pre-populated values when inputs_by_step_id was available during pre-population
|
||||
if step.is_input_type and self.inputs_by_step_id and step.id in self.outputs:
|
||||
pre_populated = self.outputs.get(step.id)
|
||||
if isinstance(pre_populated, dict) and "output" in pre_populated:
|
||||
outputs["output"] = pre_populated["output"]
|
||||
|
||||
# Output not yet set
|
||||
if "output" not in outputs:
|
||||
if self.inputs_by_step_id:
|
||||
step_id = step.id
|
||||
if step_id not in self.inputs_by_step_id:
|
||||
default_value = step.get_input_default_value(NO_REPLACEMENT)
|
||||
outputs["output"] = default_value
|
||||
elif self.inputs_by_step_id[step_id] is not None or "output" not in outputs:
|
||||
outputs["output"] = self.inputs_by_step_id[step_id]
|
||||
else:
|
||||
# When inputs_by_step_id is None (e.g., during recovery), use default
|
||||
outputs["output"] = step.get_input_default_value(NO_REPLACEMENT)
|
||||
|
||||
if step.label and step.type == "parameter_input" and "output" in outputs:
|
||||
self.runtime_replacements[step.label] = str(outputs["output"])
|
||||
@@ -651,6 +685,32 @@ class WorkflowProgress:
|
||||
raise MessageException(f"Failed to find persisted subworkflow invocation for step [{step.order_index + 1}]")
|
||||
return subworkflow_invocation
|
||||
|
||||
def _ensure_input_step_outputs_populated(self, step: "WorkflowStep") -> None:
|
||||
"""Pre-populate outputs for input steps that haven't executed yet.
|
||||
|
||||
Input steps have no dependencies, so their output value can be determined
|
||||
immediately. This allows subworkflows to access parent input values before
|
||||
the input step formally executes.
|
||||
"""
|
||||
if not step.is_input_type or step.id in self.outputs:
|
||||
return
|
||||
|
||||
# Check if step already executed - if so, skip pre-population
|
||||
step_invocations = self.workflow_invocation.step_invocations_by_step_id()
|
||||
if step.id in step_invocations:
|
||||
invocation_step = step_invocations[step.id]
|
||||
if invocation_step.state == "scheduled":
|
||||
return
|
||||
|
||||
# Determine output value from inputs_by_step_id or default
|
||||
outputs = {}
|
||||
if step.id not in self.inputs_by_step_id:
|
||||
outputs["output"] = step.get_input_default_value(NO_REPLACEMENT)
|
||||
else:
|
||||
outputs["output"] = self.inputs_by_step_id[step.id]
|
||||
|
||||
self.outputs[step.id] = outputs
|
||||
|
||||
def subworkflow_invoker(
|
||||
self,
|
||||
trans: "WorkRequestContext",
|
||||
|
||||
@@ -16,6 +16,7 @@ from galaxy_test.base.decorators import requires_new_user
|
||||
from galaxy_test.base.populators import (
|
||||
DatasetCollectionPopulator,
|
||||
DatasetPopulator,
|
||||
skip_without_tool,
|
||||
)
|
||||
from ._framework import ApiTestCase
|
||||
|
||||
@@ -427,6 +428,86 @@ class TestDatasetCollectionsApi(ApiTestCase):
|
||||
assert row_1[0] == 45
|
||||
# TODO: test case where column definition does not match supplied data
|
||||
|
||||
@skip_without_tool("cat1")
|
||||
def test_sample_sheet_map_over_preserves_columns(self, history_id):
|
||||
"""Test that mapping cat1 over a sample sheet preserves columns metadata."""
|
||||
# Create a sample sheet collection with columns metadata
|
||||
contents = [
|
||||
("sample1", "content1"),
|
||||
("sample2", "content2"),
|
||||
("sample3", "content3"),
|
||||
]
|
||||
sample_sheet_identifiers = self.dataset_collection_populator.list_identifiers(history_id, contents)
|
||||
payload = dict(
|
||||
name="test sample sheet",
|
||||
instance_type="history",
|
||||
history_id=history_id,
|
||||
element_identifiers=sample_sheet_identifiers,
|
||||
collection_type="sample_sheet",
|
||||
column_definitions=[
|
||||
{"type": "int", "name": "replicate", "optional": False},
|
||||
{"type": "string", "name": "condition", "optional": False},
|
||||
],
|
||||
rows={
|
||||
"sample1": [1, "control"],
|
||||
"sample2": [2, "treatment"],
|
||||
"sample3": [3, "control"],
|
||||
},
|
||||
)
|
||||
create_response = self._post("dataset_collections", payload, json=True)
|
||||
sample_sheet = self._check_create_response(create_response)
|
||||
hdca_id = sample_sheet["id"]
|
||||
|
||||
# Verify the input sample sheet has columns metadata
|
||||
input_elements = sample_sheet["elements"]
|
||||
assert len(input_elements) == 3
|
||||
assert input_elements[0]["columns"] == [1, "control"]
|
||||
assert input_elements[1]["columns"] == [2, "treatment"]
|
||||
assert input_elements[2]["columns"] == [3, "control"]
|
||||
|
||||
# Run cat1 on the sample sheet collection in batch mode (mapping over it)
|
||||
inputs = {
|
||||
"input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
|
||||
}
|
||||
run = self.dataset_populator.run_tool("cat1", inputs=inputs, history_id=history_id)
|
||||
self.dataset_populator.wait_for_history_jobs(history_id)
|
||||
|
||||
# Get the implicit output collection
|
||||
implicit_collections = run["implicit_collections"]
|
||||
assert len(implicit_collections) == 1, f"Expected 1 implicit collection, got {len(implicit_collections)}"
|
||||
output_collection = implicit_collections[0]
|
||||
|
||||
# Fetch the full collection details including elements
|
||||
collection_details = self.dataset_populator.get_history_collection_details(
|
||||
history_id, content_id=output_collection["id"]
|
||||
)
|
||||
|
||||
# Verify that the output collection preserved the columns metadata
|
||||
output_elements = collection_details["elements"]
|
||||
assert len(output_elements) == 3, f"Expected 3 output elements, got {len(output_elements)}"
|
||||
|
||||
# Check that columns metadata was preserved for each element
|
||||
self._assert_has_keys(output_elements[0], "columns")
|
||||
assert output_elements[0]["columns"] == [
|
||||
1,
|
||||
"control",
|
||||
], f"Expected [1, 'control'], got {output_elements[0]['columns']}"
|
||||
assert output_elements[0]["element_identifier"] == "sample1"
|
||||
|
||||
self._assert_has_keys(output_elements[1], "columns")
|
||||
assert output_elements[1]["columns"] == [
|
||||
2,
|
||||
"treatment",
|
||||
], f"Expected [2, 'treatment'], got {output_elements[1]['columns']}"
|
||||
assert output_elements[1]["element_identifier"] == "sample2"
|
||||
|
||||
self._assert_has_keys(output_elements[2], "columns")
|
||||
assert output_elements[2]["columns"] == [
|
||||
3,
|
||||
"control",
|
||||
], f"Expected [3, 'control'], got {output_elements[2]['columns']}"
|
||||
assert output_elements[2]["element_identifier"] == "sample3"
|
||||
|
||||
def test_workbook_download(self):
|
||||
xlsx_file = self.dataset_collection_populator.download_workbook(
|
||||
"sample_sheet",
|
||||
|
||||
@@ -5528,6 +5528,100 @@ test_data:
|
||||
assert_ok=True,
|
||||
)
|
||||
|
||||
def test_run_subworkflow_with_optional_parent_input_connected_but_not_provided(self):
|
||||
"""Test subworkflow when parent's optional input is connected but not provided.
|
||||
|
||||
This test verifies the fix for a bug where:
|
||||
1. Parent workflow has an OPTIONAL input
|
||||
2. That optional input IS CONNECTED to the subworkflow's input
|
||||
3. But NO DATA is provided for the parent's optional input
|
||||
4. Subworkflow has DELAYED SCHEDULING (via $link)
|
||||
|
||||
After the fix, the parent's optional input outputs are pre-populated with NO_REPLACEMENT
|
||||
before the subworkflow executes, allowing it to properly handle the missing value.
|
||||
|
||||
This is different from the case where subworkflow inputs are completely
|
||||
unconnected, which was fixed in 2022.
|
||||
"""
|
||||
with self.dataset_populator.test_history() as history_id:
|
||||
# Workflow with OPTIONAL input that IS CONNECTED to subworkflow
|
||||
# input data is not provided
|
||||
workflow = """
|
||||
class: GalaxyWorkflow
|
||||
inputs:
|
||||
parent_required:
|
||||
type: data
|
||||
parent_optional:
|
||||
type: data
|
||||
optional: true
|
||||
steps:
|
||||
nested_workflow:
|
||||
in:
|
||||
required_input: parent_required
|
||||
optional_input: parent_optional
|
||||
run:
|
||||
class: GalaxyWorkflow
|
||||
inputs:
|
||||
required_input: data
|
||||
optional_input:
|
||||
type: data
|
||||
optional: true
|
||||
steps:
|
||||
expression:
|
||||
tool_id: expression_parse_int
|
||||
state:
|
||||
input1: 1
|
||||
head:
|
||||
tool_id: head
|
||||
in:
|
||||
input: required_input
|
||||
state:
|
||||
lineNum:
|
||||
$link: expression/out1
|
||||
count_multi_file:
|
||||
tool_id: count_multi_file
|
||||
in:
|
||||
input1:
|
||||
- optional_input
|
||||
- head/out_file1
|
||||
test_data:
|
||||
parent_required:
|
||||
value: 1.bed
|
||||
type: File
|
||||
"""
|
||||
|
||||
# After the fix, this should now succeed
|
||||
summary = self._run_workflow(
|
||||
workflow,
|
||||
history_id=history_id,
|
||||
wait=True,
|
||||
assert_ok=True,
|
||||
)
|
||||
|
||||
# Check parent invocation
|
||||
parent_invocation = self.workflow_populator.get_invocation(summary.invocation_id, step_details=True)
|
||||
|
||||
# Get the subworkflow invocation
|
||||
subworkflow_step = None
|
||||
for step in parent_invocation["steps"]:
|
||||
if step.get("subworkflow_invocation_id"):
|
||||
subworkflow_step = step
|
||||
break
|
||||
|
||||
assert subworkflow_step is not None, "No subworkflow step found"
|
||||
|
||||
subworkflow_invocation_id = subworkflow_step["subworkflow_invocation_id"]
|
||||
subworkflow_invocation = self.workflow_populator.get_invocation(subworkflow_invocation_id)
|
||||
|
||||
# The subworkflow should have succeeded
|
||||
assert (
|
||||
subworkflow_invocation["state"] == "scheduled"
|
||||
), f"Expected subworkflow to succeed, got state: {subworkflow_invocation['state']}"
|
||||
|
||||
# Should not have error messages
|
||||
messages = subworkflow_invocation.get("messages", [])
|
||||
assert len(messages) == 0, f"Expected no error messages, got: {messages}"
|
||||
|
||||
def test_run_with_non_optional_data_unspecified_fails_invocation(self):
|
||||
with self.dataset_populator.test_history() as history_id:
|
||||
error = self._run_jobs(
|
||||
|
||||
@@ -254,6 +254,7 @@ class MockCollectionElement:
|
||||
self.element_identifier = element_identifier
|
||||
self.child_collection = collection
|
||||
self.hda = None
|
||||
self.columns = None
|
||||
|
||||
|
||||
class MockHDAElement:
|
||||
@@ -261,6 +262,7 @@ class MockHDAElement:
|
||||
self.element_identifier = element_identifier
|
||||
self.child_collection = False
|
||||
self.hda = object()
|
||||
self.columns = None
|
||||
|
||||
|
||||
collection_instance = MockCollectionInstance
|
||||
|
||||
Reference in New Issue
Block a user