diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix index 838c4ae802a8..92eda1d1dd13 100644 --- a/pkgs/applications/science/biology/delly/default.nix +++ b/pkgs/applications/science/biology/delly/default.nix @@ -1,19 +1,39 @@ -{ lib, stdenv, fetchFromGitHub, htslib, zlib, bzip2, xz, ncurses, boost }: +{ lib +, stdenv +, fetchFromGitHub +, boost +, bzip2 +, htslib +, llvmPackages +, xz +, zlib +, delly +, runCommand +}: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "delly"; version = "1.1.6"; src = fetchFromGitHub { - owner = "dellytools"; - repo = pname; - rev = "v${version}"; - sha256 = "sha256-/I//7MhsC/CcBeIJblzbjXp/yOSBm83KWJsrYpl6UJk="; + owner = "dellytools"; + repo = "delly"; + rev = "v${finalAttrs.version}"; + hash = "sha256-/I//7MhsC/CcBeIJblzbjXp/yOSBm83KWJsrYpl6UJk="; }; - buildInputs = [ zlib htslib bzip2 xz ncurses boost ]; + buildInputs = [ + boost + bzip2 + htslib + xz + zlib + ] ++ lib.optional stdenv.isDarwin llvmPackages.openmp; - EBROOTHTSLIB = htslib; + makeFlags = [ + "EBROOTHTSLIB=${htslib}" + "PARALLEL=1" + ]; installPhase = '' runHook preInstall @@ -23,11 +43,20 @@ stdenv.mkDerivation rec { runHook postInstall ''; + passthru.tests = { + simple = runCommand "${finalAttrs.pname}-test" { } '' + mkdir $out + ${lib.getExe delly} call -g ${delly.src}/example/ref.fa ${delly.src}/example/sr.bam > $out/sr.vcf + ${lib.getExe delly} lr -g ${delly.src}/example/ref.fa ${delly.src}/example/lr.bam > $out/lr.vcf + ${lib.getExe delly} cnv -g ${delly.src}/example/ref.fa -m ${delly.src}/example/map.fa.gz ${delly.src}/example/sr.bam > cnv.vcf + ''; + }; + meta = with lib; { description = "Structural variant caller for mapped DNA sequenced data"; license = licenses.bsd3; maintainers = with maintainers; [ scalavision ]; - platforms = platforms.linux; + platforms = platforms.unix; longDescription = '' Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, @@ -37,4 +66,4 @@ stdenv.mkDerivation rec { genomic rearrangements throughout the genome. ''; }; -} +})