95 lines
2.3 KiB
Nix
95 lines
2.3 KiB
Nix
{ lib
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, fetchFromGitHub
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, fetchpatch
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, python3Packages
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, runtimeShell
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, bcftools
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, htslib
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}:
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let
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ssshtest = fetchFromGitHub {
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owner = "ryanlayer";
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repo = "ssshtest";
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rev = "d21f7f928a167fca6e2eb31616673444d15e6fd0";
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hash = "sha256-zecZHEnfhDtT44VMbHLHOhRtNsIMWeaBASupVXtmrks=";
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};
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in python3Packages.buildPythonApplication rec {
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pname = "truvari";
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version = "4.0.0";
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src = fetchFromGitHub {
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owner = "ACEnglish";
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repo = "truvari";
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rev = "v${version}";
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hash = "sha256-UJNMKEV5m2jFqnWvkVAtymkcE2TjPIXp7JqRZpMSqsE=";
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};
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patches = [
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(fetchpatch {
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name = "fix-anno-trf-on-darwin.patch";
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url = "https://github.com/ACEnglish/truvari/commit/f9f36305e8eaa88f951562210e3672a4d4f71265.patch";
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hash = "sha256-7O9jTQDCC2b8hUBm0qJQCYMzTC9NFtn/E0dTHSfJALU=";
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})
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(fetchpatch {
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name = "fix-anno-grm-on-darwin.patch";
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url = "https://github.com/ACEnglish/truvari/commit/31416552008a506204ed4e2add55474f10392357.patch";
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hash = "sha256-42u0ewZU38GCoSfff+XQFv9hEFeO3WlJufTHcl6vkN4=";
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})
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];
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postPatch = ''
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substituteInPlace setup.py \
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--replace "rich==" "rich>="
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substituteInPlace truvari/utils.py \
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--replace "/bin/bash" "${runtimeShell}"
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patchShebangs repo_utils/test_files
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'';
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propagatedBuildInputs = with python3Packages; [
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rich
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edlib
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pysam
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intervaltree
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joblib
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numpy
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pytabix
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bwapy
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pandas
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];
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makeWrapperArgs = [
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"--prefix" "PATH" ":" (lib.makeBinPath [ bcftools htslib ])
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];
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pythonImportsCheck = [ "truvari" ];
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nativeCheckInputs = [
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bcftools
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htslib
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] ++ (with python3Packages; [
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coverage
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]);
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checkPhase = ''
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runHook preCheck
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ln -s ${ssshtest}/ssshtest .
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bash repo_utils/truvari_ssshtests.sh
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runHook postCheck
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'';
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meta = with lib; {
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description = "Structural variant comparison tool for VCFs";
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homepage = "https://github.com/ACEnglish/truvari";
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license = licenses.mit;
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maintainers = with maintainers; [ natsukium scalavision ];
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longDescription = ''
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Truvari is a benchmarking tool for comparison sets of SVs.
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It can calculate the recall, precision, and f-measure of a
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vcf from a given structural variant caller. The tool
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is created by Spiral Genetics.
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'';
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};
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}
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