svaba: init at 1.1.0

pkgs/applications/science/biology/svaba/default.nix

@@ -0,0 +1,42 @@
+{ stdenv, zlib, bzip2, lzma, fetchFromGitHub } :
+
+stdenv.mkDerivation rec {
+  version = "1.1.0";
+  pname = "svaba";
+
+  src = fetchFromGitHub {
+    owner = "walaj";
+    repo = pname;
+    rev = version;
+    sha256 = "1vv5mc9z5d22kgdy7mm27ya5aahnqgkcrskdr2405058ikk9g8kp";
+    fetchSubmodules = true;
+  };
+
+  buildInputs = [ zlib bzip2 lzma ];
+
+  installPhase = ''
+    runHook preInstall
+    install -Dm555 src/svaba/svaba $out/bin/svaba
+    runHook postInstall
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Structural variant and INDEL caller for DNA sequencing data, using genome-wide local assembly";
+    license = licenses.gpl3;
+    homepage = "https://github.com/walaj/svaba";
+    maintainers = with maintainers; [ scalavision ];
+    platforms = platforms.linux;
+    longDescription = ''
+      SvABA is a method for detecting structural variants in sequencing data
+      using genome-wide local assembly. Under the hood, SvABA uses a custom
+      implementation of SGA (String Graph Assembler) by Jared Simpson,
+      and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window
+      (with some small overlap) for every region in the genome.
+      The default is to use only clipped, discordant, unmapped and indel reads,
+      although this can be customized to any set of reads at the command line using VariantBam rules.
+      These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants.
+      Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.
+    '';
+
+  };
+}

pkgs/top-level/all-packages.nix

@@ -23687,6 +23687,8 @@ in
 
   SPAdes = callPackage ../applications/science/biology/spades { };
 
+  svaba = callPackage ../applications/science/biology/svaba { };
+
   trimal = callPackage ../applications/science/biology/trimal { };
 
   truvari = callPackage ../applications/science/biology/truvari { };