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