104 lines
2.5 KiB
Nix
104 lines
2.5 KiB
Nix
{ lib
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, fetchFromGitHub
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, python3
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, runtimeShell
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}:
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python3.pkgs.buildPythonApplication rec {
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pname = "snakemake";
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version = "8.11.0";
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format = "setuptools";
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src = fetchFromGitHub {
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owner = "snakemake";
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repo = pname;
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rev = "refs/tags/v${version}";
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hash = "sha256-bAzhQMGI4t/ftcZnz6h/PmlDlGgMU8vFVHb9QXED/Hw=";
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# https://github.com/python-versioneer/python-versioneer/issues/217
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postFetch = ''
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sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#'
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'';
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};
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postPatch = ''
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patchShebangs --build tests/
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patchShebangs --host snakemake/executors/jobscript.sh
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substituteInPlace snakemake/shell.py \
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--replace "/bin/sh" "${runtimeShell}"
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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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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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requests-mock
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snakemake-executor-plugin-cluster-generic
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];
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disabledTestPaths = [
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"tests/test_conda_python_3_7_script/test_script.py"
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];
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disabledTests = [
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"test_deploy_sources"
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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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