52 lines
1.2 KiB
Nix
52 lines
1.2 KiB
Nix
{ lib
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, fetchFromGitHub
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, python3Packages
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}:
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python3Packages.buildPythonApplication rec {
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pname = "truvari";
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version = "2.1.1";
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src = fetchFromGitHub {
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owner = "spiralgenetics";
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repo = "truvari";
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rev = "v${version}";
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sha256 = "14nsdbj063qm175xxixs34cihvsiskc9gym8pg7gbwsh13k5a00h";
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};
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postPatch = ''
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substituteInPlace setup.py \
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--replace 'python-Levenshtein==0.12.1' 'python-Levenshtein>=0.12.1'
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'';
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propagatedBuildInputs = with python3Packages; [
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pyvcf
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python-Levenshtein
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progressbar2
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pysam
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pyfaidx
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intervaltree
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pytabix
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acebinf
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bwapy
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joblib
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pandas
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];
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# no tests
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doCheck = false;
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pythonImportsCheck = [ "truvari" ];
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meta = with lib; {
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description = "Structural variant comparison tool for VCFs";
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homepage = "https://github.com/spiralgenetics/truvari";
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license = licenses.mit;
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maintainers = with maintainers; [ scalavision ];
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longDescription = ''
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Truvari is a benchmarking tool for comparison sets of SVs.
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It can calculate the recall, precision, and f-measure of a
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vcf from a given structural variant caller. The tool
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is created by Spiral Genetics.
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'';
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};
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}
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