From 77dc1504a277b3bcd28e5870bfe9583e1839fc48 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Thu, 2 May 2024 18:44:09 +0900
Subject: [PATCH 1/4] migrate: format with nixfmt

---
 .../science/biology/migrate/default.nix       | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/science/biology/migrate/default.nix b/pkgs/applications/science/biology/migrate/default.nix
index 31e4eb2fcb42..88e659a96d3d 100644
--- a/pkgs/applications/science/biology/migrate/default.nix
+++ b/pkgs/applications/science/biology/migrate/default.nix
@@ -1,4 +1,11 @@
-{ stdenv, lib, gccStdenv, fetchurl, zlib, mpi }:
+{
+  stdenv,
+  lib,
+  gccStdenv,
+  fetchurl,
+  zlib,
+  mpi,
+}:
 
 gccStdenv.mkDerivation rec {
   version = "3.7.2";
@@ -9,9 +16,15 @@ gccStdenv.mkDerivation rec {
     sha256 = "1p2364ffjc56i82snzvjpy6pkf6wvqwvlvlqxliscx2c303fxs8v";
   };
 
-  buildInputs = [ zlib mpi ];
+  buildInputs = [
+    zlib
+    mpi
+  ];
   setSourceRoot = "sourceRoot=$(echo */src)";
-  buildFlags = [ "thread" "mpis" ];
+  buildFlags = [
+    "thread"
+    "mpis"
+  ];
   preInstall = "mkdir -p $out/man/man1";
 
   meta = with lib; {

From e789c579c10b838f4894fd3d8eaf226211570720 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Thu, 2 May 2024 19:07:53 +0900
Subject: [PATCH 2/4] migrate: 3.7.2 -> 5.0.6

---
 pkgs/applications/science/biology/migrate/default.nix | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pkgs/applications/science/biology/migrate/default.nix b/pkgs/applications/science/biology/migrate/default.nix
index 88e659a96d3d..9d4865a4b9e1 100644
--- a/pkgs/applications/science/biology/migrate/default.nix
+++ b/pkgs/applications/science/biology/migrate/default.nix
@@ -8,12 +8,12 @@
 }:
 
 gccStdenv.mkDerivation rec {
-  version = "3.7.2";
+  version = "5.0.6";
   pname = "migrate";
 
   src = fetchurl {
-    url = "https://peterbeerli.com/migrate-html5/download_version3/${pname}-${version}.src.tar.gz";
-    sha256 = "1p2364ffjc56i82snzvjpy6pkf6wvqwvlvlqxliscx2c303fxs8v";
+    url = "https://peterbeerli.com/migrate-html5/download_version4/${pname}-${version}.src.tar.gz";
+    hash = "sha256-twkoR9L6VPUye12OC0B5w0PxcxyKain6RkhCswLEdwg=";
   };
 
   buildInputs = [

From f5d23a16edf9ae205ef73139c6145e44d144fe13 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Thu, 2 May 2024 19:08:25 +0900
Subject: [PATCH 3/4] migrate: add meta.mainProgram

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

diff --git a/pkgs/applications/science/biology/migrate/default.nix b/pkgs/applications/science/biology/migrate/default.nix
index 9d4865a4b9e1..e9284f62b1ac 100644
--- a/pkgs/applications/science/biology/migrate/default.nix
+++ b/pkgs/applications/science/biology/migrate/default.nix
@@ -34,5 +34,6 @@ gccStdenv.mkDerivation rec {
     license = licenses.mit;
     maintainers = [ maintainers.bzizou ];
     platforms = platforms.unix;
+    mainProgram = "migrate-n";
   };
 }

From 21c42b3d39cea12839452be335f699277cc9ee30 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Thu, 2 May 2024 19:36:15 +0900
Subject: [PATCH 4/4] migrate: refactor

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

diff --git a/pkgs/applications/science/biology/migrate/default.nix b/pkgs/applications/science/biology/migrate/default.nix
index e9284f62b1ac..7820f177bfb7 100644
--- a/pkgs/applications/science/biology/migrate/default.nix
+++ b/pkgs/applications/science/biology/migrate/default.nix
@@ -1,31 +1,31 @@
 {
   stdenv,
   lib,
-  gccStdenv,
   fetchurl,
   zlib,
   mpi,
 }:
 
-gccStdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   version = "5.0.6";
   pname = "migrate";
 
   src = fetchurl {
-    url = "https://peterbeerli.com/migrate-html5/download_version4/${pname}-${version}.src.tar.gz";
+    url = "https://peterbeerli.com/migrate-html5/download_version4/${finalAttrs.pname}-${finalAttrs.version}.src.tar.gz";
     hash = "sha256-twkoR9L6VPUye12OC0B5w0PxcxyKain6RkhCswLEdwg=";
   };
 
+  sourceRoot = "migrate-${finalAttrs.version}/src";
+
   buildInputs = [
     zlib
     mpi
   ];
-  setSourceRoot = "sourceRoot=$(echo */src)";
+
   buildFlags = [
     "thread"
     "mpis"
   ];
-  preInstall = "mkdir -p $out/man/man1";
 
   meta = with lib; {
     broken = stdenv.isDarwin;
@@ -36,4 +36,4 @@ gccStdenv.mkDerivation rec {
     platforms = platforms.unix;
     mainProgram = "migrate-n";
   };
-}
+})