44 lines
1.0 KiB
Nix
44 lines
1.0 KiB
Nix
{ 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.
|
|
'';
|
|
};
|
|
}
|