snakemake: 8.20.1 -> 8.23.0 (#348616)
This commit is contained in:
Peder Bergebakken Sundt
GitHub
commit
fba4f0f724
@ -1,138 +0,0 @@
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{ lib
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, fetchPypi
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, python3
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, stress
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}:
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python3.pkgs.buildPythonApplication rec {
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pname = "snakemake";
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version = "8.20.1";
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format = "setuptools";
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src = fetchPypi {
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inherit pname version;
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hash = "sha256-adNwIA1z/TwWsa0gQb4hAsUvHInjd30sm1dYKXvvXy8=";
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};
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postPatch = ''
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patchShebangs --build tests/
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substituteInPlace tests/common.py \
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--replace-fail 'os.environ["PYTHONPATH"] = os.getcwd()' "pass" \
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--replace-fail 'del os.environ["PYTHONPATH"]' "pass"
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substituteInPlace snakemake/unit_tests/__init__.py \
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--replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'
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'';
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propagatedBuildInputs = with python3.pkgs; [
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appdirs
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configargparse
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connection-pool
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datrie
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docutils
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gitpython
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humanfriendly
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immutables
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jinja2
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jsonschema
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nbformat
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psutil
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pulp
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pygments
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pyyaml
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requests
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reretry
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smart-open
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snakemake-interface-executor-plugins
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snakemake-interface-common
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snakemake-interface-storage-plugins
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snakemake-interface-report-plugins
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stopit
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tabulate
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throttler
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toposort
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wrapt
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yte
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];
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# See
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# https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99
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# for the current basic test suite. Slurm, Tibanna and Tes require extra
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# setup.
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nativeCheckInputs = with python3.pkgs; [
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numpy
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pandas
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pytestCheckHook
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pytest-mock
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requests-mock
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snakemake-executor-plugin-cluster-generic
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snakemake-storage-plugin-fs
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stress
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];
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pytestFlagsArray = [
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"tests/tests.py"
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"tests/test_expand.py"
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"tests/test_io.py"
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"tests/test_schema.py"
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"tests/test_executor_test_suite.py"
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"tests/test_api.py"
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];
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# Some will be disabled via https://github.com/snakemake/snakemake/pull/3074
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disabledTests = [
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# requires graphviz
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"test_filegraph"
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# requires s3
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"test_storage"
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"test_default_storage"
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"test_output_file_cache_storage"
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# requires peppy and eido
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"test_pep"
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"test_modules_peppy"
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# requires perl
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"test_shadow"
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# requires snakemake-storage-plugin-http
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"test_ancient"
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"test_modules_prefix"
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# requires snakemake-storage-plugin-s3
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"test_deploy_sources"
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# requires modules
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"test_env_modules"
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# issue with locating template file
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"test_generate_unit_tests"
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# weird
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"test_strict_mode"
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"test_issue1256"
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"test_issue2574"
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"test_github_issue1384"
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# future-proofing
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"conda"
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"singularity"
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"apptainer"
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"container"
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];
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pythonImportsCheck = [
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"snakemake"
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];
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preCheck = ''
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export HOME="$(mktemp -d)"
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'';
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meta = with lib; {
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homepage = "https://snakemake.github.io";
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license = licenses.mit;
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description = "Python-based execution environment for make-like workflows";
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mainProgram = "snakemake";
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longDescription = ''
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Snakemake is a workflow management system that aims to reduce the complexity of
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creating workflows by providing a fast and comfortable execution environment,
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together with a clean and readable specification language in Python style. Snakemake
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workflows are essentially Python scripts extended by declarative code to define
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rules. Rules describe how to create output files from input files.
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'';
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maintainers = with maintainers; [ helkafen renatoGarcia veprbl ];
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};
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}
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170
pkgs/by-name/sn/snakemake/package.nix
Normal file
170
pkgs/by-name/sn/snakemake/package.nix
Normal file
@ -0,0 +1,170 @@
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{
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lib,
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stdenv,
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fetchPypi,
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python3Packages,
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stress,
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versionCheckHook,
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}:
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python3Packages.buildPythonApplication rec {
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pname = "snakemake";
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version = "8.23.0";
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pyproject = true;
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src = fetchPypi {
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inherit pname version;
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hash = "sha256-XENI9VJW62KyrxDGSwQiygggYZOu9yW2QSNyp4BO9Us=";
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};
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postPatch = ''
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patchShebangs --build tests/
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substituteInPlace tests/common.py \
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--replace-fail 'os.environ["PYTHONPATH"] = os.getcwd()' "pass" \
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--replace-fail 'del os.environ["PYTHONPATH"]' "pass"
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substituteInPlace snakemake/unit_tests/__init__.py \
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--replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'
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'';
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build-system = with python3Packages; [
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setuptools
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];
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dependencies = with python3Packages; [
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appdirs
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conda-inject
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configargparse
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connection-pool
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datrie
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docutils
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gitpython
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humanfriendly
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immutables
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jinja2
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jsonschema
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nbformat
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psutil
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pulp
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pygments
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pyyaml
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requests
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reretry
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smart-open
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snakemake-interface-executor-plugins
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snakemake-interface-common
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snakemake-interface-storage-plugins
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snakemake-interface-report-plugins
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stopit
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tabulate
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throttler
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toposort
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wrapt
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yte
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];
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# See
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# https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99
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# for the current basic test suite. Slurm, Tibanna and Tes require extra
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# setup.
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nativeCheckInputs = with python3Packages; [
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numpy
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pandas
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pytestCheckHook
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pytest-mock
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requests-mock
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snakemake-executor-plugin-cluster-generic
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snakemake-storage-plugin-fs
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stress
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versionCheckHook
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];
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versionCheckProgramArg = [ "--version" ];
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pytestFlagsArray = [
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"tests/tests.py"
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"tests/test_expand.py"
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"tests/test_io.py"
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"tests/test_schema.py"
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"tests/test_executor_test_suite.py"
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"tests/test_api.py"
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];
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disabledTests =
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[
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# FAILED tests/tests.py::test_env_modules - AssertionError: expected successful execution
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"test_ancient"
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"test_conda_create_envs_only"
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"test_env_modules"
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"test_generate_unit_tests"
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"test_modules_prefix"
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"test_strict_mode"
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# Requires perl
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"test_shadow"
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# Require peppy and eido
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"test_peppy"
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"test_modules_peppy"
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"test_pep_pathlib"
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# CalledProcessError
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"test_filegraph" # requires graphviz
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"test_github_issue1384"
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# AssertionError: assert 127 == 1
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"test_issue1256"
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"test_issue2574"
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# Require `snakemake-storage-plugin-fs` (circular dependency)
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"test_default_storage"
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"test_default_storage_local_job"
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"test_deploy_sources"
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"test_output_file_cache_storage"
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"test_storage"
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]
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++ lib.optionals stdenv.isDarwin [
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# Unclear failure:
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# AssertionError: expected successful execution
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# `__darwinAllowLocalNetworking` doesn't help
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"test_excluded_resources_not_submitted_to_cluster"
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"test_group_job_resources_with_pipe"
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"test_group_jobs_resources"
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"test_group_jobs_resources_with_limited_resources"
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"test_group_jobs_resources_with_max_threads"
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"test_issue850"
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"test_issue860"
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"test_multicomp_group_jobs"
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"test_queue_input"
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"test_queue_input_dryrun"
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"test_queue_input_forceall"
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"test_resources_submitted_to_cluster"
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"test_scopes_submitted_to_cluster"
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];
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pythonImportsCheck = [
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"snakemake"
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];
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preCheck = ''
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export HOME="$(mktemp -d)"
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'';
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meta = {
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homepage = "https://snakemake.github.io";
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license = lib.licenses.mit;
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description = "Python-based execution environment for make-like workflows";
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changelog = "https://github.com/snakemake/snakemake/blob/v${version}/CHANGELOG.md";
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mainProgram = "snakemake";
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longDescription = ''
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Snakemake is a workflow management system that aims to reduce the complexity of
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creating workflows by providing a fast and comfortable execution environment,
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together with a clean and readable specification language in Python style. Snakemake
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workflows are essentially Python scripts extended by declarative code to define
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rules. Rules describe how to create output files from input files.
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'';
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maintainers = with lib.maintainers; [
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helkafen
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renatoGarcia
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veprbl
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];
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};
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}
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47
pkgs/development/python-modules/conda-inject/default.nix
Normal file
47
pkgs/development/python-modules/conda-inject/default.nix
Normal file
@ -0,0 +1,47 @@
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{
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lib,
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buildPythonPackage,
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fetchFromGitHub,
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# build-system
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poetry-core,
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# dependencies
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pyyaml,
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}:
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buildPythonPackage rec {
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pname = "conda-inject";
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version = "1.3.2";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "koesterlab";
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repo = "conda-inject";
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rev = "refs/tags/v${version}";
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hash = "sha256-M4+bz7ZuHlcF8tF5kSCUjjkIHG75eCCW1IJxcwxNL6o=";
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};
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build-system = [
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poetry-core
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];
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dependencies = [
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pyyaml
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];
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pythonImportsCheck = [
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"conda_inject"
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];
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# no tests
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doCheck = false;
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meta = {
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description = "Helper functions for injecting a conda environment into the current python environment";
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homepage = "https://github.com/koesterlab/conda-inject";
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changelog = "https://github.com/koesterlab/conda-inject/blob/${src.rev}/CHANGELOG.md";
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license = lib.licenses.mit;
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maintainers = with lib.maintainers; [ GaetanLepage ];
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};
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}
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@ -10,19 +10,19 @@
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buildPythonPackage rec {
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pname = "snakemake-interface-executor-plugins";
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version = "9.2.0";
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format = "pyproject";
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version = "9.3.2";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "snakemake";
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repo = pname;
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repo = "snakemake-interface-executor-plugins";
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rev = "refs/tags/v${version}";
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hash = "sha256-WMbJP17YnDzFVcr6YepT5Ltw+Jo6PPn7ayIrjx2k+go=";
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hash = "sha256-3XdsEnL+kuYhNOeAxkAsjTJ2R6NOtq97zPhQg9kdFkI=";
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};
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nativeBuildInputs = [ poetry-core ];
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build-system = [ poetry-core ];
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propagatedBuildInputs = [
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dependencies = [
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argparse-dataclass
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throttler
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snakemake-interface-common
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@ -30,10 +30,11 @@ buildPythonPackage rec {
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pythonImportsCheck = [ "snakemake_interface_executor_plugins" ];
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meta = with lib; {
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meta = {
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description = "This package provides a stable interface for interactions between Snakemake and its executor plugins";
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homepage = "https://github.com/snakemake/snakemake-interface-executor-plugins";
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license = licenses.mit;
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maintainers = with maintainers; [ veprbl ];
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changelog = "https://github.com/snakemake/snakemake-interface-executor-plugins/blob/${src.rev}/CHANGELOG.md";
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license = lib.licenses.mit;
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maintainers = with lib.maintainers; [ veprbl ];
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};
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}
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@ -18387,8 +18387,6 @@ with pkgs;
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smc = callPackage ../tools/misc/smc { };
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snakemake = callPackage ../applications/science/misc/snakemake { };
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snore = callPackage ../tools/misc/snore { };
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snzip = callPackage ../tools/archivers/snzip { };
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@ -2514,6 +2514,8 @@ self: super: with self; {
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conda = callPackage ../development/python-modules/conda { };
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conda-inject = callPackage ../development/python-modules/conda-inject { };
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conda-libmamba-solver = callPackage ../development/python-modules/conda-libmamba-solver { };
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conda-package-handling = callPackage ../development/python-modules/conda-package-handling { };
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@ -14536,7 +14538,7 @@ self: super: with self; {
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});
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snakemake = toPythonModule (pkgs.snakemake.override {
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python3 = python;
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python3Packages = self;
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});
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snakemake-executor-plugin-cluster-generic = callPackage ../development/python-modules/snakemake-executor-plugin-cluster-generic { };
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Block a user