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{ lib
, python3
, fetchFromGitHub
}:
python3.pkgs.buildPythonApplication rec {
pname = "deeptools";
version = "3.5.4";
pyproject = true;
src = fetchFromGitHub {
owner = "deeptools";
repo = "deepTools";
rev = version;
hash = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI=";
};
nativeBuildInputs = with python3.pkgs; [
setuptools
];
propagatedBuildInputs = with python3.pkgs; [
numpy
numpydoc
scipy
py2bit
pybigwig
pysam
matplotlib
plotly
deeptoolsintervals
importlib-metadata
];
nativeCheckInputs = with python3.pkgs; [
pytestCheckHook
];
preCheck = ''
export PATH="$out/bin:$PATH"
'';
disabledTestPaths = [
# tests trip on `len(sys.argv) == 1`
"deeptools/test/test_bigwigAverage.py"
"deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py"
"deeptools/test/test_heatmapper.py"
"deeptools/test/test_multiBamSummary.py"
];
meta = with lib; {
homepage = "https://deeptools.readthedocs.io/en/develop";
description = "Tools for exploring deep DNA sequencing data";
longDescription = ''
deepTools contains useful modules to process the mapped reads data for multiple
quality checks, creating normalized coverage files in standard bedGraph and bigWig
file formats, that allow comparison between different files (for example, treatment and control).
Finally, using such normalized and standardized files, deepTools can create many
publication-ready visualizations to identify enrichments and for functional
annotations of the genome.
'';
license = with licenses; [ mit bsd3 ];
maintainers = with maintainers; [ scalavision ];
};
}
|