From 9139eb5aeeb11cd3bce46f8c8a4984698331b56e Mon Sep 17 00:00:00 2001
From: Pavol Rusnak <pavol@rusnak.io>
Date: Sat, 2 Jan 2021 20:15:25 +0100
Subject: [PATCH] bowtie2: 2.3.5.1 -> 2.4.2

---
 .../applications/science/biology/bowtie2/default.nix | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix
index dc818e2fb86..603e5892ff1 100644
--- a/pkgs/applications/science/biology/bowtie2/default.nix
+++ b/pkgs/applications/science/biology/bowtie2/default.nix
@@ -1,19 +1,19 @@
-{ stdenv, fetchFromGitHub, zlib, tbb, python, perl }:
+{ stdenv, fetchFromGitHub, cmake, tbb, zlib }:
 
 stdenv.mkDerivation rec {
   pname = "bowtie2";
-  version = "2.3.5.1";
+  version = "2.4.2";
 
   src = fetchFromGitHub {
     owner = "BenLangmead";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1l1f0yhjqqvy4lpxfml1xwv7ayimwbpzazvp0281gb4jb5f5mr1a";
+    sha256 = "11apzq7l1lk3yxw97g9dfr0gwnvfh58x6apifcblgd66gbip3y1y";
   };
 
-  buildInputs = [ zlib tbb python perl ];
+  nativeBuildInputs = [ cmake ];
 
-  installFlags = [ "prefix=$(out)" ];
+  buildInputs = [ tbb zlib ];
 
   meta = with stdenv.lib; {
     description = "An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences";
@@ -21,6 +21,6 @@ stdenv.mkDerivation rec {
     homepage = "http://bowtie-bio.sf.net/bowtie2";
     maintainers = with maintainers; [ rybern ];
     platforms = platforms.all;
-    broken = stdenv.isAarch64;
+    broken = stdenv.isAarch64; # only x86 is supported
   };
 }