From 4d211a3e8bfb20942df214a393f2a3fe3efb0ba1 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Thu, 5 Dec 2024 13:19:58 +0000 Subject: [PATCH] Explicitly add cwl-utils to dependencies Imported e.g. in `lib/galaxy/tools/expressions/evaluation.py` . No actual change to requirements files as it's already included as a dependency of cwltool. --- lib/galaxy_ext/expressions/handle_job.py | 2 +- packages/app/setup.cfg | 1 + pyproject.toml | 1 + 3 files changed, 3 insertions(+), 1 deletion(-) diff --git a/lib/galaxy_ext/expressions/handle_job.py b/lib/galaxy_ext/expressions/handle_job.py index fc9838d381b9..e125501757d1 100644 --- a/lib/galaxy_ext/expressions/handle_job.py +++ b/lib/galaxy_ext/expressions/handle_job.py @@ -27,7 +27,7 @@ def run(environment_path=None): if expression is None: - raise Exception("Python library cwltool must be available to evaluate expressions.") + raise Exception("Python library cwl-utils must be available to evaluate expressions.") if environment_path is None: environment_path = os.environ.get("GALAXY_EXPRESSION_INPUTS") diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index 1e6b7ca57d3f..80a292225e7c 100644 --- a/packages/app/setup.cfg +++ b/packages/app/setup.cfg @@ -49,6 +49,7 @@ install_requires = bx-python celery cloudauthz==0.6.0 + cwl-utils dparse gxformat2 kombu>=5.3 diff --git a/pyproject.toml b/pyproject.toml index be857e903b7f..08ba68afcd48 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,6 +30,7 @@ dependencies = [ "circus", "conda-package-streaming", "CT3>=3.3.3", # Python 3.13 support + "cwl-utils>=0.13", "cwltool>=3.1.20230624081518", # save time, minimum needed by cwl-1.0 branch "dictobj", "dnspython",