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{ lib
, fetchFromGitHub
, fetchpatch
, python3Packages
, runtimeShell
, bcftools
, htslib
}:
let
ssshtest = fetchFromGitHub {
owner = "ryanlayer";
repo = "ssshtest";
rev = "d21f7f928a167fca6e2eb31616673444d15e6fd0";
hash = "sha256-zecZHEnfhDtT44VMbHLHOhRtNsIMWeaBASupVXtmrks=";
};
in python3Packages.buildPythonApplication rec {
pname = "truvari";
version = "4.0.0";
src = fetchFromGitHub {
owner = "ACEnglish";
repo = "truvari";
rev = "v${version}";
hash = "sha256-UJNMKEV5m2jFqnWvkVAtymkcE2TjPIXp7JqRZpMSqsE=";
};
patches = [
(fetchpatch {
name = "fix-anno-trf-on-darwin.patch";
url = "https://github.com/ACEnglish/truvari/commit/f9f36305e8eaa88f951562210e3672a4d4f71265.patch";
hash = "sha256-7O9jTQDCC2b8hUBm0qJQCYMzTC9NFtn/E0dTHSfJALU=";
})
(fetchpatch {
name = "fix-anno-grm-on-darwin.patch";
url = "https://github.com/ACEnglish/truvari/commit/31416552008a506204ed4e2add55474f10392357.patch";
hash = "sha256-42u0ewZU38GCoSfff+XQFv9hEFeO3WlJufTHcl6vkN4=";
})
];
postPatch = ''
substituteInPlace setup.py \
--replace "rich==" "rich>="
substituteInPlace truvari/utils.py \
--replace "/bin/bash" "${runtimeShell}"
patchShebangs repo_utils/test_files
'';
propagatedBuildInputs = with python3Packages; [
rich
edlib
pysam
intervaltree
joblib
numpy
pytabix
bwapy
pandas
];
makeWrapperArgs = [
"--prefix" "PATH" ":" (lib.makeBinPath [ bcftools htslib ])
];
pythonImportsCheck = [ "truvari" ];
nativeCheckInputs = [
bcftools
htslib
] ++ (with python3Packages; [
coverage
]);
checkPhase = ''
runHook preCheck
ln -s ${ssshtest}/ssshtest .
bash repo_utils/truvari_ssshtests.sh
runHook postCheck
'';
meta = with lib; {
description = "Structural variant comparison tool for VCFs";
homepage = "https://github.com/ACEnglish/truvari";
license = licenses.mit;
maintainers = with maintainers; [ natsukium 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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