nixpkgs/pkgs/applications/science/biology/truvari/default.nix
scalavision 535a7006ea truvari: init at 1.3.2 (#70877)
pythonPackages.pyvcf: init at 0.6.8
2019-10-24 17:06:42 -04:00

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{ lib
, fetchFromGitHub
, python3Packages
}:
python3Packages.buildPythonApplication rec {
pname = "truvari";
version = "1.3.2";
src = fetchFromGitHub {
owner = "spiralgenetics";
repo = "truvari";
rev = "v${version}";
sha256 = "0wmjz8nzibvj0ixky1m0qi7iyd204prk7glbvig1cvaab33k19f1";
};
propagatedBuildInputs = with python3Packages; [
pyvcf
python-Levenshtein
progressbar2
pysam
pyfaidx
intervaltree
];
prePatch = ''
substituteInPlace ./setup.py \
--replace '"progressbar2==3.41.0",' "" \
--replace '"pysam==0.15.2",' ""
'';
meta = with lib; {
description = "Structural variant comparison tool for VCFs";
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.
'';
};
}