84 lines
1.9 KiB
Nix
84 lines
1.9 KiB
Nix
{ lib
|
|
, fetchFromGitHub
|
|
, python3
|
|
}:
|
|
|
|
python3.pkgs.buildPythonApplication rec {
|
|
pname = "snakemake";
|
|
version = "7.25.3";
|
|
format = "setuptools";
|
|
|
|
src = fetchFromGitHub {
|
|
owner = "snakemake";
|
|
repo = pname;
|
|
rev = "refs/tags/v${version}";
|
|
hash = "sha256-KrstajTocVX5Tw7aiPoJ9vxJ0nKF+jqJcYJKrJvBt0Q=";
|
|
};
|
|
|
|
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
|
|
];
|
|
|
|
disabledTestPaths = [
|
|
"tests/test_slurm.py"
|
|
"tests/test_tes.py"
|
|
"tests/test_tibanna.py"
|
|
"tests/test_linting.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 ];
|
|
};
|
|
}
|