From ae95c0d5a57143feb3aaac76aa694b906288c05d Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Fri, 14 Jul 2023 00:10:19 +0900
Subject: [PATCH] delly: refactor

---
 .../science/biology/delly/default.nix         | 38 ++++++++++++++-----
 1 file changed, 28 insertions(+), 10 deletions(-)

diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix
index 871c9bd4cdde..2cde00036604 100644
--- a/pkgs/applications/science/biology/delly/default.nix
+++ b/pkgs/applications/science/biology/delly/default.nix
@@ -1,19 +1,37 @@
-{ lib, stdenv, fetchFromGitHub, htslib, zlib, bzip2, xz, ncurses, boost, runCommand, delly }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, boost
+, bzip2
+, htslib
+, xz
+, zlib
+, delly
+, runCommand
+}:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "delly";
   version = "1.1.6";
 
   src = fetchFromGitHub {
-      owner = "dellytools";
-      repo = pname;
-      rev = "v${version}";
-      sha256 = "sha256-/I//7MhsC/CcBeIJblzbjXp/yOSBm83KWJsrYpl6UJk=";
+    owner = "dellytools";
+    repo = "delly";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-/I//7MhsC/CcBeIJblzbjXp/yOSBm83KWJsrYpl6UJk=";
   };
 
-  buildInputs = [ zlib htslib bzip2 xz ncurses boost ];
+  buildInputs = [
+    boost
+    bzip2
+    htslib
+    xz
+    zlib
+  ];
 
-  EBROOTHTSLIB = htslib;
+  makeFlags = [
+    "EBROOTHTSLIB=${htslib}"
+  ];
 
   installPhase = ''
     runHook preInstall
@@ -24,7 +42,7 @@ stdenv.mkDerivation rec {
   '';
 
   passthru.tests = {
-    simple = runCommand "${pname}-test" { } ''
+    simple = runCommand "${finalAttrs.pname}-test" { } ''
       mkdir $out
       ${lib.getExe delly} call -g ${delly.src}/example/ref.fa ${delly.src}/example/sr.bam > $out/sr.vcf
       ${lib.getExe delly} lr -g ${delly.src}/example/ref.fa ${delly.src}/example/lr.bam > $out/lr.vcf
@@ -46,4 +64,4 @@ stdenv.mkDerivation rec {
       genomic rearrangements throughout the genome.
     '';
   };
-}
+})