From fdc1ddd305b92850fdf8e2ad1c06bf8f6dc26916 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Fri, 14 Jul 2023 16:38:10 +0900
Subject: [PATCH 1/3] kssd: 1.1 -> 2.21

Diff: https://github.com/yhg926/public_kssd/compare/v1.1...v2.21
---
 pkgs/applications/science/biology/kssd/default.nix | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/pkgs/applications/science/biology/kssd/default.nix b/pkgs/applications/science/biology/kssd/default.nix
index 34d997252f5b..579042ec50bc 100644
--- a/pkgs/applications/science/biology/kssd/default.nix
+++ b/pkgs/applications/science/biology/kssd/default.nix
@@ -2,22 +2,21 @@
 
 stdenv.mkDerivation rec {
   pname = "kssd";
-  version = "1.1";
+  version = "2.21";
 
   src = fetchFromGitHub {
     owner = "yhg926";
     repo = "public_kssd";
     rev = "v${version}";
-    sha256 = "sha256-8jzYqo9LXF66pQ1EIusm+gba2VbTYpJz2K3NVlA3QxY=";
+    hash = "sha256-D/s1jL2oKE0rSdRMVljskYFsw5UPOv1L95Of+K+e17w=";
   };
 
   patches = [
-    # Pull upstream patch for -fno-common toolchain support:
-    #   https://github.com/yhg926/public_kssd/pull/9
+    # https://github.com/yhg926/public_kssd/pull/11
     (fetchpatch {
-      name = "fno-common.patch";
-      url = "https://github.com/yhg926/public_kssd/commit/cdd1e8aae256146f5913a3b4c723b638d53bdf27.patch";
-      sha256 = "sha256-HhaTRqPfKR+ouh0PwEH6u22pbuqbX2OypRzw8BXm0W4=";
+      name = "allocate-enough-memory.patch";
+      url = "https://github.com/yhg926/public_kssd/commit/b1e66bbcc04687bc3201301cd742a0b26a87cb5d.patch";
+      hash = "sha256-yFyJetpsGKeu+H6Oxrmn5ea4ESVtblb3YJDja4JEAEM=";
     })
   ];
 

From 847c506eaece0913d4ca995e34bd4c84bac1cb19 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Fri, 14 Jul 2023 17:29:33 +0900
Subject: [PATCH 2/3] kssd: refactor

---
 .../science/biology/kssd/default.nix          | 23 +++++++++++++------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/pkgs/applications/science/biology/kssd/default.nix b/pkgs/applications/science/biology/kssd/default.nix
index 579042ec50bc..200b70458ed3 100644
--- a/pkgs/applications/science/biology/kssd/default.nix
+++ b/pkgs/applications/science/biology/kssd/default.nix
@@ -1,13 +1,18 @@
-{ lib, stdenv, fetchFromGitHub, fetchpatch, zlib, automake, autoconf, libtool }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, fetchpatch
+, zlib
+}:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "kssd";
   version = "2.21";
 
   src = fetchFromGitHub {
     owner = "yhg926";
     repo = "public_kssd";
-    rev = "v${version}";
+    rev = "v${finalAttrs.version}";
     hash = "sha256-D/s1jL2oKE0rSdRMVljskYFsw5UPOv1L95Of+K+e17w=";
   };
 
@@ -20,11 +25,14 @@ stdenv.mkDerivation rec {
     })
   ];
 
-  nativeBuildInputs = [ autoconf automake ];
-  buildInputs = [ zlib libtool ];
+  buildInputs = [ zlib ];
 
   installPhase = ''
-      install -vD kssd $out/bin/kssd
+    runHook preInstall
+
+    install -vD kssd $out/bin/kssd
+
+    runHook postInstall
   '';
 
   meta = with lib; {
@@ -33,5 +41,6 @@ stdenv.mkDerivation rec {
     homepage    = "https://github.com/yhg926/public_kssd";
     maintainers = with maintainers; [ unode ];
     platforms = [ "x86_64-linux" ];
+    mainProgram = "kssd";
   };
-}
+})

From 10c3a4062187989d425cd4b0e8ef7e59377e1b6d Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Fri, 3 Nov 2023 18:00:30 +0900
Subject: [PATCH 3/3] kssd: enable aarch64-linux support & tests

---
 pkgs/applications/science/biology/kssd/default.nix | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/pkgs/applications/science/biology/kssd/default.nix b/pkgs/applications/science/biology/kssd/default.nix
index 200b70458ed3..8f60b8b991ed 100644
--- a/pkgs/applications/science/biology/kssd/default.nix
+++ b/pkgs/applications/science/biology/kssd/default.nix
@@ -3,6 +3,8 @@
 , fetchFromGitHub
 , fetchpatch
 , zlib
+, kssd
+, runCommand
 }:
 
 stdenv.mkDerivation (finalAttrs: {
@@ -35,12 +37,21 @@ stdenv.mkDerivation (finalAttrs: {
     runHook postInstall
   '';
 
+  passthru.tests = {
+    simple = runCommand "${finalAttrs.pname}-test" { } ''
+      mkdir $out
+      ${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -r ${kssd.src}/test_fna/seqs1 -o $out/reference
+      ${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -o $out/query ${kssd.src}/test_fna/seqs2
+      ${lib.getExe kssd} dist -r $out/reference -o $out/distout $out/query
+    '';
+  };
+
   meta = with lib; {
     description = "K-mer substring space decomposition";
     license     = licenses.asl20;
     homepage    = "https://github.com/yhg926/public_kssd";
     maintainers = with maintainers; [ unode ];
-    platforms = [ "x86_64-linux" ];
+    platforms = platforms.linux;
     mainProgram = "kssd";
   };
 })