79 lines
1.5 KiB
Nix
79 lines
1.5 KiB
Nix
{
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lib,
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buildPythonPackage,
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fetchFromGitHub,
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fetchpatch,
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swig,
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cython,
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matplotlib,
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numpy,
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pandas,
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pysam,
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setuptools,
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pytestCheckHook,
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nix-update-script,
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}:
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buildPythonPackage rec {
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pname = "htseq";
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version = "2.0.4";
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pyproject = true;
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src = fetchFromGitHub {
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owner = "htseq";
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repo = "htseq";
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rev = "release_${version}";
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hash = "sha256-7ocrmuj9LOtPz9XbI5rKGcdE5JbFz/pZh00Nie65XxE=";
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};
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patches = [
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# https://github.com/htseq/htseq/pull/84
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(fetchpatch {
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name = "replace-distutils-with-sysconfig.patch";
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url = "https://github.com/htseq/htseq/commit/f0f1e464ee9aee56f0b44f905e7b3355b0bb8f29.patch";
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hash = "sha256-yDYkXCPy+YFgnk1rnXwCB998aZwVd5nJeejZIgeEzAo=";
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})
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];
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nativeBuildInputs = [ swig ];
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build-system = [
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cython
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numpy
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pysam
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setuptools
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];
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dependencies = [
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numpy
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pysam
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];
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optional-dependencies = {
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htseq-qa = [ matplotlib ];
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};
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pythonImportsCheck = [ "HTSeq" ];
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nativeCheckInputs = [
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pandas
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pytestCheckHook
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] ++ optional-dependencies.htseq-qa;
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preCheck = ''
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rm -r src HTSeq
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export PATH=$out/bin:$PATH
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'';
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passthru.updateScript = nix-update-script {
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extraArgs = [
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"--version-regex"
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"release_(.+)"
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];
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};
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meta = with lib; {
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homepage = "https://htseq.readthedocs.io/";
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description = "Framework to work with high-throughput sequencing data";
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maintainers = with maintainers; [ unode ];
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};
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}
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