From 72d675b23cf1c8326818499805ca7eca432d0cfe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Arcadio=20Rubio=20Garc=C3=ADa?= <arc@well.ox.ac.uk>
Date: Mon, 22 Jan 2018 18:27:50 +0000
Subject: [PATCH] star: init at 2.5.3a

---
 lib/maintainers.nix                           |  1 +
 .../science/biology/star/default.nix          | 34 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 3 files changed, 37 insertions(+)
 create mode 100644 pkgs/applications/science/biology/star/default.nix

diff --git a/lib/maintainers.nix b/lib/maintainers.nix
index 9f9234f18a55..1e50e3d93f71 100644
--- a/lib/maintainers.nix
+++ b/lib/maintainers.nix
@@ -55,6 +55,7 @@
   antonxy = "Anton Schirg <anton.schirg@posteo.de>";
   apeschar = "Albert Peschar <albert@peschar.net>";
   apeyroux = "Alexandre Peyroux <alex@px.io>";
+  arcadio = "Arcadio Rubio García <arc@well.ox.ac.uk>";
   ardumont = "Antoine R. Dumont <eniotna.t@gmail.com>";
   aristid = "Aristid Breitkreuz <aristidb@gmail.com>";
   arobyn = "Alexei Robyn <shados@shados.net>";
diff --git a/pkgs/applications/science/biology/star/default.nix b/pkgs/applications/science/biology/star/default.nix
new file mode 100644
index 000000000000..1642739140d6
--- /dev/null
+++ b/pkgs/applications/science/biology/star/default.nix
@@ -0,0 +1,34 @@
+{ stdenv, fetchFromGitHub, zlib }:
+
+stdenv.mkDerivation rec {
+  name = "star-${version}";
+  version = "2.5.3a";
+
+  src = fetchFromGitHub {
+    repo = "STAR";
+    owner = "alexdobin";
+    rev = version;
+    sha256 = "1fd9xl7i1zxgsxn2qf6gz8s42g2djm29qmp6qb35d8nnxh8ns54x";
+  };
+
+  sourceRoot = "source/source";
+  
+  postPatch = "sed 's:/bin/rm:rm:g' -i Makefile";
+  
+  buildInputs = [ zlib ];
+  
+  buildPhase = "make STAR STARlong";
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp STAR STARlong $out/bin
+  '';
+  
+  meta = with stdenv.lib; {
+    description = "Spliced Transcripts Alignment to a Reference";
+    homepage = https://github.com/alexdobin/STAR;
+    license = licenses.gpl3Plus;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.arcadio ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 6318a56fedf4..186ce06978f2 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -18962,6 +18962,8 @@ with pkgs;
 
   snpeff = callPackage ../applications/science/biology/snpeff/default.nix { };
 
+  star = callPackage ../applications/science/biology/star { };
+
   varscan = callPackage ../applications/science/biology/varscan/default.nix { };
 
   bwa = callPackage ../applications/science/biology/bwa/default.nix { };