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571c71e6f7
We are migrating packages that meet below requirements:
1. using `callPackage`
2. called path is a directory
3. overriding set is empty (`{ }`)
4. not containing path expressions other than relative path (to
makenixpkgs-vet happy)
5. not referenced by nix files outside of the directory, other
than`pkgs/top-level/all-packages.nix`
6. not referencing nix files outside of the directory
7. not referencing `default.nix` (since it's changed to `package.nix`)
8. `outPath` doesn't change after migration
The tool is here: https://github.com/Aleksanaa/by-name-migrate.
39 lines
1.2 KiB
Nix
39 lines
1.2 KiB
Nix
{lib, stdenv, fetchurl, jre, makeWrapper}:
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stdenv.mkDerivation rec {
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pname = "varscan";
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version = "2.4.6";
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src = fetchurl {
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url = "https://github.com/dkoboldt/varscan/raw/master/VarScan.v${version}.jar";
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sha256 = "sha256-6CcjC0epbKsDXFxxeOUImSGh4cjR5INqawL/iOOkwqs=";
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};
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nativeBuildInputs = [ makeWrapper ];
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buildInputs = [ jre ];
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dontUnpack = true;
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installPhase = ''
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mkdir -p $out/libexec/varscan
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cp $src $out/libexec/varscan/varscan.jar
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mkdir -p $out/bin
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makeWrapper ${jre}/bin/java $out/bin/varscan --add-flags "-jar $out/libexec/varscan/varscan.jar"
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'';
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meta = with lib; {
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description = "Variant calling and somatic mutation/CNV detection for next-generation sequencing data";
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# VarScan 2 is free for non-commercial use by academic,
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# government, and non-profit/not-for-profit institutions. A
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# commercial version of the software is available, and licensed
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# through the Office of Technology Management at Washington
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# University School of Medicine.
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license = licenses.unfree;
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homepage = "https://github.com/dkoboldt/varscan";
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sourceProvenance = with sourceTypes; [ binaryBytecode ];
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maintainers = with maintainers; [ jbedo ];
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platforms = platforms.all;
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};
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}
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