From 29bc617bacc261daa0e12f7042a6713014ad96cc Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 29 Oct 2025 13:46:18 +0100 Subject: [PATCH 1/2] add missing enable_beta_tool_formats config option --- doc/source/admin/galaxy_options.rst | 12 ++++++++++++ lib/galaxy/config/sample/galaxy.yml.sample | 8 +++++++- lib/galaxy/config/schemas/config_schema.yml | 7 +++++++ 3 files changed, 26 insertions(+), 1 deletion(-) diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 1ca46ebcb9e4..7bcb6ef7cbf3 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -5842,4 +5842,16 @@ :Type: int +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +``enable_beta_tool_formats`` +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +:Description: + Enable user defined tools. In order to enable users to use this + feature create a role of type `Custom Tool Execution` in the admin + user interface and assign users or groups to this role. +:Default: ``false`` +:Type: bool + + diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index 7f5da5718ffc..e1b5efd19d3a 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -23,7 +23,8 @@ gravity: # Process manager to use. # ``supervisor`` is the default process manager when Gravity is invoked as a non-root user. # ``systemd`` is the default when Gravity is invoked as root. - # Valid options are: supervisor, systemd + # ``multiprocessing`` is the default when Gravity is invoked as the foreground shortcut ``galaxy`` instead of ``galaxyctl`` + # Valid options are: supervisor, systemd, multiprocessing # process_manager: # What command to write to the process manager configs @@ -3104,3 +3105,8 @@ galaxy: # ``true``. Runs in a Celery task. #failed_jobs_working_directory_cleanup_interval: 86400 + # Enable user defined tools. In order to enable users to use this + # feature create a role of type `Custom Tool Execution` in the admin + # user interface and assign users or groups to this role. + #enable_beta_tool_formats: false + diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml index 98b49e587f54..a1f2b92268d7 100644 --- a/lib/galaxy/config/schemas/config_schema.yml +++ b/lib/galaxy/config/schemas/config_schema.yml @@ -4301,3 +4301,10 @@ mapping: default: 86400 desc: | The interval in seconds between attempts to delete all failed Galaxy job's working directories from the filesystem (every 24 hours by default) if enable_failed_jobs_working_directory_cleanup is ``true``. Runs in a Celery task. + + enable_beta_tool_formats: + type: bool + default: false + required: false + desc: | + Enable user defined tools. In order to enable users to use this feature create a role of type `Custom Tool Execution` in the admin user interface and assign users or groups to this role. \ No newline at end of file From 029a5409f4c64e3b896fe533b95e31d207481bfd Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 20 Nov 2025 15:33:06 +0100 Subject: [PATCH 2/2] reformulate --- doc/source/admin/galaxy_options.rst | 5 ++--- lib/galaxy/config/sample/galaxy.yml.sample | 5 ++--- lib/galaxy/config/schemas/config_schema.yml | 2 +- 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 7bcb6ef7cbf3..90e2973aa139 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -5847,9 +5847,8 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :Description: - Enable user defined tools. In order to enable users to use this - feature create a role of type `Custom Tool Execution` in the admin - user interface and assign users or groups to this role. + Enable beta tool formats (yaml, cwl, ...) which is a prerequisite + for user defined tools. :Default: ``false`` :Type: bool diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index e1b5efd19d3a..809bf678ff28 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -3105,8 +3105,7 @@ galaxy: # ``true``. Runs in a Celery task. #failed_jobs_working_directory_cleanup_interval: 86400 - # Enable user defined tools. In order to enable users to use this - # feature create a role of type `Custom Tool Execution` in the admin - # user interface and assign users or groups to this role. + # Enable beta tool formats (yaml, cwl, ...) which is a prerequisite + # for user defined tools. #enable_beta_tool_formats: false diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml index a1f2b92268d7..dc00f6e2c64b 100644 --- a/lib/galaxy/config/schemas/config_schema.yml +++ b/lib/galaxy/config/schemas/config_schema.yml @@ -4307,4 +4307,4 @@ mapping: default: false required: false desc: | - Enable user defined tools. In order to enable users to use this feature create a role of type `Custom Tool Execution` in the admin user interface and assign users or groups to this role. \ No newline at end of file + Enable beta tool formats (yaml, cwl, ...) which is a prerequisite for user defined tools. \ No newline at end of file