From 3d860972eefe10e04b7994d85f88dc7aeb6db248 Mon Sep 17 00:00:00 2001
From: scalavision <scalavision@gmail.com>
Date: Fri, 11 Oct 2019 04:08:45 +0200
Subject: [PATCH] delly: init at 0.8.1 (#70871)

---
 .../science/biology/delly/default.nix         | 40 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 42 insertions(+)
 create mode 100644 pkgs/applications/science/biology/delly/default.nix

diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix
new file mode 100644
index 000000000000..bfdf5a1bb17e
--- /dev/null
+++ b/pkgs/applications/science/biology/delly/default.nix
@@ -0,0 +1,40 @@
+{ stdenv, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }:
+
+stdenv.mkDerivation rec {
+  pname = "delly";
+  version = "0.8.1";
+
+  src = fetchFromGitHub {
+      owner = "dellytools";
+      repo = pname;
+      rev = "v${version}";
+      sha256 = "18gm86j1g1k4z1cjv2m5v9rsl1xqs2w3dhwcsnzx2mhkrvmlc4i1";
+  };
+
+  buildInputs = [ zlib htslib bzip2 lzma ncurses boost ];
+
+  EBROOTHTSLIB = htslib;
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm555 src/delly $out/bin/delly
+
+    runHook postInstall
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Structural variant caller for mapped DNA sequenced data";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ scalavision ];
+    platforms = platforms.linux;
+    longDescription = ''
+      Delly is an integrated structural variant (SV) prediction method
+      that can discover, genotype and visualize deletions, tandem duplications,
+      inversions and translocations at single-nucleotide resolution in
+      short-read massively parallel sequencing data. It uses paired-ends,
+      split-reads and read-depth to sensitively and accurately delineate
+      genomic rearrangements throughout the genome.
+    '';
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 4e84b42bf093..6a9a6c39996f 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -23005,6 +23005,8 @@ in
   conglomerate = callPackage ../applications/science/biology/conglomerate { };
 
   dcm2niix = callPackage ../applications/science/biology/dcm2niix { };
+  
+  delly = callPackage ../applications/science/biology/delly { };
 
   diamond = callPackage ../applications/science/biology/diamond { };