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{ lib
, fetchFromGitHub
, python3
}:
python3.pkgs.buildPythonApplication rec {
pname = "snakemake";
version = "7.32.4";
format = "setuptools";
src = fetchFromGitHub {
owner = "snakemake";
repo = pname;
rev = "refs/tags/v${version}";
hash = "sha256-9KuMPqvM8ZCTuomc0R9MBxsK3KIpukDTrlwU6MHysK0=";
};
propagatedBuildInputs = with python3.pkgs; [
appdirs
configargparse
connection-pool
datrie
docutils
gitpython
humanfriendly
jinja2
jsonschema
nbformat
psutil
pulp
pyyaml
requests
reretry
smart-open
stopit
tabulate
throttler
toposort
wrapt
yte
];
# See
# https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99
# for the current basic test suite. Slurm, Tibanna and Tes require extra
# setup.
nativeCheckInputs = with python3.pkgs; [
pandas
pytestCheckHook
requests-mock
pillow
];
disabledTestPaths = [
"tests/test_slurm.py"
"tests/test_tes.py"
"tests/test_tibanna.py"
"tests/test_linting.py"
"tests/test_google_lifesciences.py"
"tests/test_conda_python_script/test_script.py"
];
disabledTests = [
# Tests require network access
"test_github_issue1396"
"test_github_issue1460"
];
pythonImportsCheck = [
"snakemake"
];
meta = with lib; {
homepage = "https://snakemake.github.io";
license = licenses.mit;
description = "Python-based execution environment for make-like workflows";
longDescription = ''
Snakemake is a workflow management system that aims to reduce the complexity of
creating workflows by providing a fast and comfortable execution environment,
together with a clean and readable specification language in Python style. Snakemake
workflows are essentially Python scripts extended by declarative code to define
rules. Rules describe how to create output files from input files.
'';
maintainers = with maintainers; [ helkafen renatoGarcia veprbl ];
};
}
|