diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml index 0a3050cbcb6b..981a44cf9a8d 100644 --- a/.github/workflows/osx_startup.yaml +++ b/.github/workflows/osx_startup.yaml @@ -49,9 +49,10 @@ jobs: with: path: .tox key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-osx - - name: Install miniconda # use this job to test using Python from a conda environment + - name: Install miniforge # use this job to test using Python from a conda environment uses: conda-incubator/setup-miniconda@v3 with: + miniforge-version: latest activate-environment: '' - name: Restore client cache uses: actions/cache@v4 diff --git a/doc/source/admin/dependency_resolvers.rst b/doc/source/admin/dependency_resolvers.rst index 19862f4c7c23..88821e74fa5d 100644 --- a/doc/source/admin/dependency_resolvers.rst +++ b/doc/source/admin/dependency_resolvers.rst @@ -207,7 +207,7 @@ debug ensure_channels Conda channels to enable by default. See https://conda.io/docs/user-guide/tasks/manage-channels.html for more information about channels. This defaults to the value of the global ``conda_ensure_channels`` option or - ``iuc,conda-forge,bioconda,defaults`` otherwise. This order should be consistent with the `Bioconda prescribed + ``conda-forge,bioconda`` otherwise. This order should be consistent with the `Bioconda prescribed order `__ if it includes ``bioconda``. auto_install diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index cdf82ab688fd..1b55117668f4 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -477,7 +477,7 @@ :Description: conda channels to enable by default (https://conda.io/docs/user-guide/tasks/manage-channels.html) -:Default: ``conda-forge,bioconda,defaults`` +:Default: ``conda-forge,bioconda`` :Type: str diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index bb4c6fc32d4f..55a1d5388234 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -578,7 +578,7 @@ galaxy: # conda channels to enable by default # (https://conda.io/docs/user-guide/tasks/manage-channels.html) - #conda_ensure_channels: conda-forge,bioconda,defaults + #conda_ensure_channels: conda-forge,bioconda # Use locally-built conda packages. #conda_use_local: false diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml index aa7f4891936d..5e0d2e352487 100644 --- a/lib/galaxy/config/schemas/config_schema.yml +++ b/lib/galaxy/config/schemas/config_schema.yml @@ -359,7 +359,7 @@ mapping: conda_ensure_channels: type: str - default: conda-forge,bioconda,defaults + default: conda-forge,bioconda required: false desc: | conda channels to enable by default diff --git a/lib/galaxy/tool_util/deps/conda_util.py b/lib/galaxy/tool_util/deps/conda_util.py index 4905b6091e3e..8bead7148a5d 100644 --- a/lib/galaxy/tool_util/deps/conda_util.py +++ b/lib/galaxy/tool_util/deps/conda_util.py @@ -60,13 +60,10 @@ def conda_link() -> str: else: url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh" else: - if sys.maxsize > 2**32: - if "arm64" in platform.platform(): - url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh" - else: - url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" + if "arm64" in platform.platform(): + url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh" else: - url = "https://repo.anaconda.com/miniconda/Miniconda3-4.5.12-Linux-x86.sh" + url = "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" return url @@ -75,21 +72,12 @@ def find_conda_prefix() -> str: for Miniconda installs. """ home = os.path.expanduser("~") - miniconda_2_dest = os.path.join(home, "miniconda2") - miniconda_3_dest = os.path.join(home, "miniconda3") - anaconda_2_dest = os.path.join(home, "anaconda2") - anaconda_3_dest = os.path.join(home, "anaconda3") - # Prefer miniconda3 install if both available - if os.path.exists(miniconda_3_dest): - return miniconda_3_dest - elif os.path.exists(miniconda_2_dest): - return miniconda_2_dest - elif os.path.exists(anaconda_3_dest): - return anaconda_3_dest - elif os.path.exists(anaconda_2_dest): - return anaconda_2_dest - else: - return miniconda_3_dest + destinations = ["miniforge3", "miniconda3", "miniconda2", "anaconda3", "anaconda2"] + for destination in destinations: + destination = os.path.join(home, destination) + if os.path.exists(destination): + return destination + return os.path.join(home, "miniforge3") class CondaContext(installable.InstallableContext):