From 01ddcaa879471f82eb5f8e704897e272a8206786 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sat, 13 May 2023 17:51:01 +0900
Subject: [PATCH 1/3] bwa: 0.7.17 -> unstable-2022-09-23

Diff: https://github.com/lh3/bwa/compare/v0.7.17...139f68fc4c3747813783a488aef2adc86626b01b
---
 .../science/biology/bwa/default.nix           | 26 +++++++------------
 1 file changed, 9 insertions(+), 17 deletions(-)

diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix
index d9ae226027a..aeea7ed2646 100644
--- a/pkgs/applications/science/biology/bwa/default.nix
+++ b/pkgs/applications/science/biology/bwa/default.nix
@@ -1,24 +1,16 @@
-{ lib, stdenv, fetchurl, fetchpatch, zlib }:
+{ lib, stdenv, fetchFromGitHub, zlib }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "bwa";
-  version = "0.7.17";
+  version = "unstable-2022-09-23";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/bio-bwa/${pname}-${version}.tar.bz2";
-    sha256 = "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy";
+  src = fetchFromGitHub {
+    owner = "lh3";
+    repo = "bwa";
+    rev = "139f68fc4c3747813783a488aef2adc86626b01b";
+    hash = "sha256-8u35lTK6gBKeapYoIkG9MuJ/pyy/HFA2OiPn+Ml2C6c=";
   };
 
-  patches = [
-    # Pull upstream patch for -fno-common toolchain support like upstream
-    # gcc-10: https://github.com/lh3/bwa/pull/267
-    (fetchpatch {
-      name  = "fno-common.patch";
-      url = "https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch";
-      sha256 = "1lihfxai6vcshv5vr3m7yhk833bdivkja3gld6ilwrc4z28f6wqy";
-    })
-  ];
-
   buildInputs = [ zlib ];
 
   # Avoid hardcoding gcc to allow environments with a different
@@ -45,6 +37,6 @@ stdenv.mkDerivation rec {
     license     = licenses.gpl3;
     homepage    = "https://bio-bwa.sourceforge.net/";
     maintainers = with maintainers; [ luispedro ];
-    platforms = platforms.x86_64;
+    platforms = platforms.unix;
   };
 }

From c85dced23e4d0a0a860371880aad0d8bca83ed6f Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sat, 13 May 2023 17:55:53 +0900
Subject: [PATCH 2/3] bwa: update license

---
 pkgs/applications/science/biology/bwa/default.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix
index aeea7ed2646..36bf2288c54 100644
--- a/pkgs/applications/science/biology/bwa/default.nix
+++ b/pkgs/applications/science/biology/bwa/default.nix
@@ -34,7 +34,7 @@ stdenv.mkDerivation {
 
   meta = with lib; {
     description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome";
-    license     = licenses.gpl3;
+    license     = licenses.gpl3Plus;
     homepage    = "https://bio-bwa.sourceforge.net/";
     maintainers = with maintainers; [ luispedro ];
     platforms = platforms.unix;

From 04dd7f41e720c10c48ba65f60a3063740fe081c8 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sat, 13 May 2023 17:57:16 +0900
Subject: [PATCH 3/3] bwa: add runHook

---
 pkgs/applications/science/biology/bwa/default.nix | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix
index 36bf2288c54..4786f25beb5 100644
--- a/pkgs/applications/science/biology/bwa/default.nix
+++ b/pkgs/applications/science/biology/bwa/default.nix
@@ -24,12 +24,16 @@ stdenv.mkDerivation {
   # it's unclear which headers are intended to be part of the public interface
   # so we may find ourselves having to add more here over time
   installPhase = ''
+    runHook preInstall
+
     install -vD -t $out/bin bwa
     install -vD -t $out/lib libbwa.a
     install -vD -t $out/include bntseq.h
     install -vD -t $out/include bwa.h
     install -vD -t $out/include bwamem.h
     install -vD -t $out/include bwt.h
+
+    runHook postInstall
   '';
 
   meta = with lib; {