pyrox.dev
multiqc: init at 1.26 (#372510)
authored by Pol Dellaiera and committed by GitHub 83defbad 1de313a3
+117
pkgs/by-name/mu/multiqc/package.nix
+117
pkgs/by-name/mu/multiqc/package.nix
···
···
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{
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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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}:
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python3Packages.buildPythonApplication rec {
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pname = "multiqc";
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version = "1.26";
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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-MPAw6gG/3LzdskkDXOTDEM1NpG0sH9GvklYFQ1ZXWIs=";
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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 = "67435083a8bfa228dca3dda7d835facef15fc2c7";
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hash = "sha256-oYmPIJSy6dOKPcMr3B4foGoWcerA29x0XeGoU4dSYsA=";
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name = "test-data";
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})
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];
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sourceRoot = "multiqc";
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dependencies = with python3Packages; [
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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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pillow
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plotly
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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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typeguard
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tqdm
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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-stub
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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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export PATH=$out/bin:$PATH
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'';
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# Some tests run subprocess.run() with "ps"
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nativeCheckInputs = with python3Packages; [
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procps
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pytest-cov
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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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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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}
+49
pkgs/development/python-modules/spectra/default.nix
+49
pkgs/development/python-modules/spectra/default.nix
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···
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{
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buildPythonPackage,
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colormath,
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fetchFromGitHub,
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fetchpatch2,
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lib,
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pytestCheckHook,
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setuptools,
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}:
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buildPythonPackage rec {
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pname = "spectra";
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version = "0.0.11";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "jsvine";
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repo = "spectra";
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tag = "v${version}";
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hash = "sha256-4A2TWTxYqckJ3DX5cd2KN3KXcmO/lQdXmOEnGi76RsA=";
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};
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patches = [
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# https://github.com/jsvine/spectra/pull/21
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(fetchpatch2 {
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name = "nose-to-pytest.patch";
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url = "https://github.com/jsvine/spectra/commit/50037aba16dac4bf0fb7ffbd787d0e6b906e8a4b.patch";
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hash = "sha256-cMoIbjRwcZjvhiIOcJR7NmIAOaqpr/e5eh9+sPGKqos=";
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excludes = [ ".github/*" ];
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})
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];
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build-system = [
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setuptools
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];
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propagatedBuildInputs = [ colormath ];
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nativeCheckInputs = [
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pytestCheckHook
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];
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meta = {
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description = "Python library that makes color math, color scales, and color-space conversion easy";
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homepage = "https://github.com/jsvine/spectra";
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license = lib.licenses.mit;
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maintainers = with lib.maintainers; [ apraga ];
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};
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}
+2
pkgs/top-level/python-packages.nix
+2
pkgs/top-level/python-packages.nix
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speaklater3 = callPackage ../development/python-modules/speaklater3 { };
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spectra = callPackage ../development/python-modules/spectra { };
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spectral-cube = callPackage ../development/python-modules/spectral-cube { };
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speechbrain = callPackage ../development/python-modules/speechbrain { };