65 lines
1.7 KiB
Nix
65 lines
1.7 KiB
Nix
{ lib
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, python3
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, fetchFromGitHub
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}:
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python3.pkgs.buildPythonApplication rec {
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pname = "deeptools";
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version = "3.5.5";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "deeptools";
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repo = "deepTools";
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rev = "refs/tags/${version}";
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hash = "sha256-2kSlL7Y5f/FjVtStnmz+GlTw2oymrtxOCaXlqgbQ7FU=";
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};
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nativeBuildInputs = with python3.pkgs; [
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setuptools
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];
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propagatedBuildInputs = with python3.pkgs; [
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numpy
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numpydoc
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scipy
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py2bit
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pybigwig
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pysam
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matplotlib
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plotly
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deeptoolsintervals
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importlib-metadata
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];
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nativeCheckInputs = with python3.pkgs; [
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pytestCheckHook
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];
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preCheck = ''
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export PATH="$out/bin:$PATH"
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'';
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disabledTestPaths = [
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# tests trip on `len(sys.argv) == 1`
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"deeptools/test/test_bigwigAverage.py"
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"deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py"
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"deeptools/test/test_heatmapper.py"
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"deeptools/test/test_multiBamSummary.py"
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];
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meta = with lib; {
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homepage = "https://deeptools.readthedocs.io/en/develop";
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description = "Tools for exploring deep DNA sequencing data";
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longDescription = ''
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deepTools contains useful modules to process the mapped reads data for multiple
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quality checks, creating normalized coverage files in standard bedGraph and bigWig
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file formats, that allow comparison between different files (for example, treatment and control).
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Finally, using such normalized and standardized files, deepTools can create many
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publication-ready visualizations to identify enrichments and for functional
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annotations of the genome.
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'';
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license = with licenses; [ mit bsd3 ];
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maintainers = with maintainers; [ scalavision ];
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};
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}
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