131 lines
3.0 KiB
Nix
131 lines
3.0 KiB
Nix
{
|
|
lib,
|
|
python3Packages,
|
|
fetchFromGitHub,
|
|
procps,
|
|
stdenv,
|
|
versionCheckHook,
|
|
addBinToPathHook,
|
|
}:
|
|
|
|
let
|
|
test-data = fetchFromGitHub {
|
|
name = "test-data";
|
|
owner = "MultiQC";
|
|
repo = "test-data";
|
|
rev = "d775b73c106d48726653f2fd02e473b7acbd93d8";
|
|
hash = "sha256-uxBpMx22gWJmnbF9tVuVIdYdiqUh7n51swzu5hnfZQ0=";
|
|
};
|
|
in
|
|
python3Packages.buildPythonApplication rec {
|
|
pname = "multiqc";
|
|
version = "1.29";
|
|
pyproject = true;
|
|
|
|
src = fetchFromGitHub {
|
|
name = "multiqc";
|
|
owner = "MultiQC";
|
|
repo = "MultiQC";
|
|
tag = "v${version}";
|
|
hash = "sha256-KKLdDNf889lEbCyNpJFZoE8rNO50CRzNP4hKpKHRAcE=";
|
|
};
|
|
|
|
# Multiqc cannot remove temporary directories in some case.
|
|
# Default is 10 retries, lower it to 2
|
|
postPatch = ''
|
|
substituteInPlace multiqc/utils/util_functions.py \
|
|
--replace-fail \
|
|
"max_retries: int = 10," \
|
|
"max_retries: int = 2,"
|
|
'';
|
|
|
|
build-system = with python3Packages; [ setuptools ];
|
|
|
|
dependencies = with python3Packages; [
|
|
boto3
|
|
click
|
|
humanize
|
|
importlib-metadata
|
|
jinja2
|
|
kaleido
|
|
markdown
|
|
numpy
|
|
packaging
|
|
requests
|
|
pillow
|
|
plotly
|
|
pyyaml
|
|
rich
|
|
rich-click
|
|
coloredlogs
|
|
spectra
|
|
pydantic
|
|
typeguard
|
|
tqdm
|
|
python-dotenv
|
|
natsort
|
|
tiktoken
|
|
jsonschema
|
|
polars
|
|
pyarrow
|
|
];
|
|
|
|
optional-dependencies = {
|
|
dev = with python3Packages; [
|
|
pre-commit-hooks
|
|
pdoc3
|
|
pytest
|
|
pytest-cov
|
|
pytest-xdist
|
|
syrupy
|
|
pygithub
|
|
mypy
|
|
types-pyyaml
|
|
types-tqdm
|
|
types-requests
|
|
types-markdown
|
|
types-beautifulsoup4
|
|
types-pillow
|
|
];
|
|
};
|
|
|
|
preCheck = ''
|
|
ln -s ${test-data} ./test-data
|
|
'';
|
|
|
|
nativeCheckInputs =
|
|
(with python3Packages; [
|
|
pytest-xdist
|
|
pytestCheckHook
|
|
])
|
|
++ [
|
|
addBinToPathHook # Some tests run subprocess.run() with "multiqc"
|
|
procps # Some tests run subprocess.run() with "ps"
|
|
versionCheckHook
|
|
];
|
|
|
|
versionCheckProgramArg = "--version";
|
|
|
|
disabledTests =
|
|
# On darwin, kaleido fails to starts
|
|
lib.optionals (stdenv.hostPlatform.isDarwin) [
|
|
"test_flat_plot"
|
|
];
|
|
|
|
meta = {
|
|
description = "Aggregates bioinformatics results from multiple samples into a unified report";
|
|
longDescription = ''
|
|
MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
|
|
|
|
Reports are generated by scanning given directories for recognised log files. These are parsed and a single HTML report is generated summarising the statistics for all logs found. MultiQC reports can describe multiple analysis steps and large numbers of samples within a single plot, and multiple analysis tools making it ideal for routine fast quality control.
|
|
'';
|
|
homepage = "https://multiqc.info";
|
|
changelog = "https://github.com/MultiQC/MultiQC/releases/tag/v${version}/";
|
|
license = [ lib.licenses.gpl3Plus ];
|
|
maintainers = [ lib.maintainers.apraga ];
|
|
mainProgram = "multiqc";
|
|
platforms = lib.platforms.unix;
|
|
};
|
|
|
|
}
|