nixpkgs/pkgs/applications/science/biology/truvari/default.nix
2020-03-02 09:15:58 +01:00

45 lines
1.1 KiB
Nix

{ lib
, fetchFromGitHub
, python3Packages
}:
python3Packages.buildPythonApplication rec {
pname = "truvari";
version = "1.3.4";
src = fetchFromGitHub {
owner = "spiralgenetics";
repo = "truvari";
rev = "v${version}";
sha256 = "1bph7v48s7pyfagz8a2fzl5fycjliqzn5lcbv3m2bp2ih1f1gd1v";
};
propagatedBuildInputs = with python3Packages; [
pyvcf
python-Levenshtein
progressbar2
pysam
pyfaidx
intervaltree
];
prePatch = ''
substituteInPlace ./setup.py \
--replace '"progressbar2==3.41.0",' '"progressbar2==3.47.0",' \
--replace '"pysam==0.15.2",' '"pysam==0.15.4",' \
--replace '"pyfaidx==0.5.5.2",' '"pyfaidx==0.5.8",'
'';
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.
'';
};
}