From bb317093e86714c78a21f57f2480da513544eb8f Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Thu, 8 Jun 2023 12:15:17 +0900
Subject: [PATCH 1/2] aragorn: 1.2.38 -> 1.2.41

- change the source and homepage
- change the license
---
 .../science/biology/aragorn/default.nix       | 28 +++++++++++++------
 1 file changed, 20 insertions(+), 8 deletions(-)

diff --git a/pkgs/applications/science/biology/aragorn/default.nix b/pkgs/applications/science/biology/aragorn/default.nix
index fa0c10b00c20..4d5b3a4d017a 100644
--- a/pkgs/applications/science/biology/aragorn/default.nix
+++ b/pkgs/applications/science/biology/aragorn/default.nix
@@ -1,27 +1,39 @@
-{ lib, stdenv, fetchurl }:
+{ lib, stdenv, fetchurl, installShellFiles }:
+let
+  man = fetchurl {
+    url = "https://web.archive.org/web/20230608093053if_/http://www.ansikte.se/ARAGORN/Downloads/aragorn.1";
+    hash = "sha256-bjD22dpkQZcGR0TwMxdpaed4VZZO2NUOoAw4o66iyS4=";
+  };
+in
 
 stdenv.mkDerivation rec {
-  version = "1.2.38";
+  version = "1.2.41";
   pname = "aragorn";
 
   src = fetchurl {
-    url = "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/${pname}${version}.tgz";
-    sha256 = "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b";
+    url = "http://www.ansikte.se/ARAGORN/Downloads/aragorn${version}.c";
+    hash = "sha256-kqMcxcCwrRbU17AZkZibd18H0oFd8TX+bj6riPXpf0o=";
   };
 
+  dontUnpack = true;
+
+  nativeBuildInputs = [
+    installShellFiles
+  ];
+
   buildPhase = ''
-    $CC -O3 -ffast-math -finline-functions -o aragorn aragorn${version}.c
+    $CC -O3 -ffast-math -finline-functions -o aragorn $src
   '';
 
   installPhase = ''
     mkdir -p $out/bin && cp aragorn $out/bin
-    mkdir -p $out/man/1 && cp aragorn.1 $out/man/1
+    installManPage ${man}
   '';
 
   meta = with lib; {
     description = "Detects tRNA, mtRNA, and tmRNA genes in nucleotide sequences";
-    homepage = "http://mbio-serv2.mbioekol.lu.se/ARAGORN/";
-    license = licenses.gpl2;
+    homepage = "http://www.ansikte.se/ARAGORN/";
+    license = licenses.gpl3Plus;
     maintainers = [ maintainers.bzizou ];
     platforms = platforms.unix;
   };

From 597e4e8652452df886c863c4ccc671ddb491ecae Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Thu, 8 Jun 2023 12:20:21 +0900
Subject: [PATCH 2/2] aragorn: fix format

- use finalAttrs instead of rec
- add runHook
---
 .../science/biology/aragorn/default.nix       | 20 +++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/pkgs/applications/science/biology/aragorn/default.nix b/pkgs/applications/science/biology/aragorn/default.nix
index 4d5b3a4d017a..4ee8501e8e13 100644
--- a/pkgs/applications/science/biology/aragorn/default.nix
+++ b/pkgs/applications/science/biology/aragorn/default.nix
@@ -1,4 +1,8 @@
-{ lib, stdenv, fetchurl, installShellFiles }:
+{ lib
+, stdenv
+, fetchurl
+, installShellFiles
+}:
 let
   man = fetchurl {
     url = "https://web.archive.org/web/20230608093053if_/http://www.ansikte.se/ARAGORN/Downloads/aragorn.1";
@@ -6,12 +10,12 @@ let
   };
 in
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   version = "1.2.41";
   pname = "aragorn";
 
   src = fetchurl {
-    url = "http://www.ansikte.se/ARAGORN/Downloads/aragorn${version}.c";
+    url = "http://www.ansikte.se/ARAGORN/Downloads/aragorn${finalAttrs.version}.c";
     hash = "sha256-kqMcxcCwrRbU17AZkZibd18H0oFd8TX+bj6riPXpf0o=";
   };
 
@@ -22,12 +26,20 @@ stdenv.mkDerivation rec {
   ];
 
   buildPhase = ''
+    runHook preBuild
+
     $CC -O3 -ffast-math -finline-functions -o aragorn $src
+
+    runHook postBuild
   '';
 
   installPhase = ''
+    runHook preInstall
+
     mkdir -p $out/bin && cp aragorn $out/bin
     installManPage ${man}
+
+    runHook postInstall
   '';
 
   meta = with lib; {
@@ -37,4 +49,4 @@ stdenv.mkDerivation rec {
     maintainers = [ maintainers.bzizou ];
     platforms = platforms.unix;
   };
-}
+})