From 9958fc16cb16acb255ad203cca2376ec180d3eec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Arcadio=20Rubio=20Garc=C3=ADa?= <arcadio@pm.me>
Date: Fri, 4 Jul 2025 19:55:50 +0200
Subject: [PATCH 1/2] minimap2: cleanup and add correct 32-bit ARM flag

---
 pkgs/by-name/mi/minimap2/package.nix | 33 ++++++++++++++++++++--------
 1 file changed, 24 insertions(+), 9 deletions(-)

diff --git a/pkgs/by-name/mi/minimap2/package.nix b/pkgs/by-name/mi/minimap2/package.nix
index 247f5b19be1a..ece612e9b74e 100644
--- a/pkgs/by-name/mi/minimap2/package.nix
+++ b/pkgs/by-name/mi/minimap2/package.nix
@@ -3,6 +3,9 @@
   stdenv,
   fetchFromGitHub,
   zlib,
+  minimap2,
+  testers,
+  nix-update-script,
 }:
 
 stdenv.mkDerivation rec {
@@ -18,24 +21,36 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ zlib ];
 
-  makeFlags = lib.optionals stdenv.hostPlatform.isAarch64 [
-    "arm_neon=1"
-    "aarch64=1"
-  ];
+  makeFlags =
+    lib.optionals stdenv.hostPlatform.isAarch [ "arm_neon=1" ]
+    ++ lib.optionals stdenv.hostPlatform.isAarch64 [ "aarch64=1" ];
 
   installPhase = ''
-    mkdir -p $out/bin
-    cp minimap2 $out/bin
-    mkdir -p $out/share/man/man1
-    cp minimap2.1 $out/share/man/man1
+    runHook preInstall
+    install -m755 -Dt $out/bin minimap2
+    install -m644 -Dt $out/share/man/man1 minimap2.1
+    runHook postInstall
   '';
 
+  passthru.tests.version = testers.testVersion {
+    package = minimap2;
+    command = "minimap2 --version";
+  };
+
+  passthru.updateScript = nix-update-script { };
+
   meta = with lib; {
     description = "Versatile pairwise aligner for genomic and spliced nucleotide sequences";
+    longDescription = ''
+      Minimap2 is a versatile sequence alignment program that aligns
+      DNA or mRNA sequences against a large reference database. It is
+      particularly efficient for long reads and can handle various
+      sequencing technologies including PacBio and Oxford Nanopore.
+    '';
     mainProgram = "minimap2";
     homepage = "https://lh3.github.io/minimap2";
     license = licenses.mit;
-    platforms = platforms.all;
+    platforms = platforms.unix;
     maintainers = [ maintainers.arcadio ];
   };
 }

From efd27f4846fc0c0b5e7a39571bc80b64652627b9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Arcadio=20Rubio=20Garc=C3=ADa?= <arcadio@pm.me>
Date: Sat, 5 Jul 2025 17:34:57 +0200
Subject: [PATCH 2/2] minimap2: cleanup and add correct 32-bit ARM flag

---
 pkgs/by-name/mi/minimap2/package.nix | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/pkgs/by-name/mi/minimap2/package.nix b/pkgs/by-name/mi/minimap2/package.nix
index ece612e9b74e..863f3be16dae 100644
--- a/pkgs/by-name/mi/minimap2/package.nix
+++ b/pkgs/by-name/mi/minimap2/package.nix
@@ -2,9 +2,9 @@
   lib,
   stdenv,
   fetchFromGitHub,
+  installShellFiles,
+  versionCheckHook,
   zlib,
-  minimap2,
-  testers,
   nix-update-script,
 }:
 
@@ -21,6 +21,8 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ zlib ];
 
+  nativeBuildInputs = [ installShellFiles ];
+
   makeFlags =
     lib.optionals stdenv.hostPlatform.isAarch [ "arm_neon=1" ]
     ++ lib.optionals stdenv.hostPlatform.isAarch64 [ "aarch64=1" ];
@@ -28,14 +30,13 @@ stdenv.mkDerivation rec {
   installPhase = ''
     runHook preInstall
     install -m755 -Dt $out/bin minimap2
-    install -m644 -Dt $out/share/man/man1 minimap2.1
+    installManPage minimap2.1
     runHook postInstall
   '';
 
-  passthru.tests.version = testers.testVersion {
-    package = minimap2;
-    command = "minimap2 --version";
-  };
+  nativeInstallCheckInputs = [ versionCheckHook ];
+  versionCheckProgramArg = "--version";
+  doInstallCheck = true;
 
   passthru.updateScript = nix-update-script { };