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146 lines
3.3 KiB
Nix
146 lines
3.3 KiB
Nix
{
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lib,
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python3Packages,
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fetchFromGitHub,
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procps,
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stdenv,
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versionCheckHook,
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addBinToPathHook,
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}:
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python3Packages.buildPythonApplication rec {
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pname = "multiqc";
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version = "1.30";
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pyproject = true;
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# Two data sources. One for the code, another for the test data
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srcs = [
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(fetchFromGitHub {
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name = "multiqc";
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owner = "MultiQC";
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repo = "MultiQC";
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tag = "v${version}";
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hash = "sha256-TR5YFoWj97gpsykIzc1lqtYVePsVLRIT0HXw+VPJ7o4=";
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})
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(fetchFromGitHub {
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owner = "MultiQC";
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repo = "test-data";
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rev = "cc9f853e7892eb537e91505e0e847ff63669138d";
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hash = "sha256-/MiNnPayG6wpF2S09ENYTlEBF7Km4aH1RjdGOfMgZcA=";
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name = "test-data";
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})
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];
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# Multiqc cannot remove temporary directories in some case.
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# Default is 10 retries, lower it to 2
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postPatch = ''
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substituteInPlace multiqc/utils/util_functions.py \
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--replace-fail \
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"max_retries: int = 10," \
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"max_retries: int = 2,"
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substituteInPlace pyproject.toml \
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--replace 'polars-lts-cpu' 'polars'
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'';
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sourceRoot = "multiqc";
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nativeBuildInputs = with python3Packages; [
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setuptools
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wheel
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];
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dependencies = with python3Packages; [
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boto3
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click
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humanize
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importlib-metadata
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jinja2
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kaleido
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markdown
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natsort
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numpy
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packaging
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requests
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polars
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pillow
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plotly
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pyarrow
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pyyaml
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rich
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rich-click
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coloredlogs
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spectra
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pydantic
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tiktoken
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typeguard
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tqdm
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python-dotenv
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jsonschema
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];
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optional-dependencies = {
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dev = with python3Packages; [
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pre-commit-hooks
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pdoc3
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pytest
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pytest-cov
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pytest-xdist
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syrupy
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pygithub
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mypy
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types-pyyaml
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types-tqdm
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types-requests
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types-markdown
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types-beautifulsoup4
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types-pillow
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];
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};
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# Some tests run subprocess.run() with "multiqc"
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preCheck = ''
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chmod -R u+w ../test-data
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ln -s ../test-data .
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'';
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# Some tests run subprocess.run() with "ps"
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nativeCheckInputs =
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with python3Packages;
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[
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pytest-cov-stub
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pytest-xdist
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pytestCheckHook
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syrupy
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pygithub
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versionCheckHook
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]
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++ [
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procps
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addBinToPathHook
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];
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versionCheckProgramArg = "--version";
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disabledTests =
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# On darwin, kaleido fails to starts
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lib.optionals (stdenv.hostPlatform.isDarwin) [
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"test_flat_plot"
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];
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meta = {
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description = "Aggregates bioinformatics results from multiple samples into a unified report";
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longDescription = ''
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MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
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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.
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'';
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homepage = "https://multiqc.info";
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changelog = "https://github.com/MultiQC/MultiQC/releases/tag/v${version}/";
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license = [ lib.licenses.gpl3Plus ];
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maintainers = [ lib.maintainers.apraga ];
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mainProgram = "multiqc";
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platforms = lib.platforms.unix;
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};
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}
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