From 5cb77278a438a9b6d497758caa3dcd0a8e795925 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sun, 28 Apr 2024 13:42:08 +0900
Subject: [PATCH 1/3] mafft: 7.525 -> 7.526

Diff: https://gitlab.com/sysimm/mafft/-/compare/v7.525...v7.526
---
 pkgs/applications/science/biology/mafft/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/biology/mafft/default.nix b/pkgs/applications/science/biology/mafft/default.nix
index f2e3ead2e913..bc9ab7ad79b3 100644
--- a/pkgs/applications/science/biology/mafft/default.nix
+++ b/pkgs/applications/science/biology/mafft/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "mafft";
-  version = "7.525";
+  version = "7.526";
 
   src = fetchFromGitLab {
     owner = "sysimm";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-ckBmvFssYAmYcBHAEftjQqBV0MB0theGfemaPx3XUws=";
+    sha256 = "sha256-VNe00r12qEkLEbpZdJCe5xZ73JA3uAmuAeG+eSeRDI0=";
   };
 
   preBuild = ''

From 4b3081c5e0de5638f547c31c7e1e5b901a50ce88 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sun, 28 Apr 2024 13:45:46 +0900
Subject: [PATCH 2/3] mafft: prettify

---
 .../science/biology/mafft/default.nix         | 36 +++++++++++--------
 1 file changed, 21 insertions(+), 15 deletions(-)

diff --git a/pkgs/applications/science/biology/mafft/default.nix b/pkgs/applications/science/biology/mafft/default.nix
index bc9ab7ad79b3..b003bb98b5f9 100644
--- a/pkgs/applications/science/biology/mafft/default.nix
+++ b/pkgs/applications/science/biology/mafft/default.nix
@@ -1,14 +1,18 @@
-{ lib, stdenv, fetchFromGitLab }:
+{
+  lib,
+  stdenv,
+  fetchFromGitLab,
+}:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "mafft";
   version = "7.526";
 
   src = fetchFromGitLab {
     owner = "sysimm";
-    repo = pname;
-    rev = "v${version}";
-    sha256 = "sha256-VNe00r12qEkLEbpZdJCe5xZ73JA3uAmuAeG+eSeRDI0=";
+    repo = "mafft";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-VNe00r12qEkLEbpZdJCe5xZ73JA3uAmuAeG+eSeRDI0=";
   };
 
   preBuild = ''
@@ -16,14 +20,16 @@ stdenv.mkDerivation rec {
     make clean
   '';
 
-  makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" "PREFIX=$(out)" ];
+  makeFlags = [
+    "CC=${stdenv.cc.targetPrefix}cc"
+    "PREFIX=$(out)"
+  ];
 
-  meta = with lib;
-    {
-      description = "Multiple alignment program for amino acid or nucleotide sequences";
-      homepage = "https://mafft.cbrc.jp/alignment/software/";
-      license = licenses.bsd3;
-      maintainers = with maintainers; [ natsukium ];
-      platforms = platforms.unix;
-    };
-}
+  meta = with lib; {
+    description = "Multiple alignment program for amino acid or nucleotide sequences";
+    homepage = "https://mafft.cbrc.jp/alignment/software/";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ natsukium ];
+    platforms = platforms.unix;
+  };
+})

From ce0af18702c144542ff7017d568d6b16c6498e9c Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sun, 28 Apr 2024 13:57:47 +0900
Subject: [PATCH 3/3] mafft: enable simple test

---
 .../science/biology/mafft/default.nix         | 20 +++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/pkgs/applications/science/biology/mafft/default.nix b/pkgs/applications/science/biology/mafft/default.nix
index b003bb98b5f9..ca1f89388a44 100644
--- a/pkgs/applications/science/biology/mafft/default.nix
+++ b/pkgs/applications/science/biology/mafft/default.nix
@@ -2,6 +2,8 @@
   lib,
   stdenv,
   fetchFromGitLab,
+  runCommand,
+  mafft,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
@@ -25,6 +27,24 @@ stdenv.mkDerivation (finalAttrs: {
     "PREFIX=$(out)"
   ];
 
+  passthru.tests = {
+    simple = runCommand "${finalAttrs.pname}-test" { } ''
+      mkdir $out
+      cd ${finalAttrs.src}/test
+      ${lib.getExe mafft} sample > $out/test.fftns2
+      ${lib.getExe mafft} --maxiterate 100  sample > $out/test.fftnsi
+      ${lib.getExe mafft} --globalpair sample > $out/test.gins1
+      ${lib.getExe mafft} --globalpair --maxiterate 100  sample > $out/test.ginsi
+      ${lib.getExe mafft} --localpair sample > $out/test.lins1
+      ${lib.getExe mafft} --localpair --maxiterate 100  sample > $out/test.linsi
+      diff $out/test.fftns2 sample.fftns2
+      diff $out/test.fftnsi sample.fftnsi
+      diff $out/test.gins1 sample.gins1
+      diff $out/test.ginsi sample.ginsi
+      diff $out/test.lins1 sample.lins1
+    '';
+  };
+
   meta = with lib; {
     description = "Multiple alignment program for amino acid or nucleotide sequences";
     homepage = "https://mafft.cbrc.jp/alignment/software/";