138 lines
3.3 KiB
Nix
138 lines
3.3 KiB
Nix
{ 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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