From 61be2ca18aa99609194a4589983a4f3747e38033 Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Thu, 13 Jul 2023 23:52:29 +0900
Subject: [PATCH 1/3] delly: enable darwin support

- add passthru.tests
---
 pkgs/applications/science/biology/delly/default.nix | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix
index 838c4ae802a8..871c9bd4cdde 100644
--- a/pkgs/applications/science/biology/delly/default.nix
+++ b/pkgs/applications/science/biology/delly/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, htslib, zlib, bzip2, xz, ncurses, boost }:
+{ lib, stdenv, fetchFromGitHub, htslib, zlib, bzip2, xz, ncurses, boost, runCommand, delly }:
 
 stdenv.mkDerivation rec {
   pname = "delly";
@@ -23,11 +23,20 @@ stdenv.mkDerivation rec {
     runHook postInstall
   '';
 
+  passthru.tests = {
+    simple = runCommand "${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
+      ${lib.getExe delly} cnv -g ${delly.src}/example/ref.fa -m ${delly.src}/example/map.fa.gz ${delly.src}/example/sr.bam > cnv.vcf
+    '';
+  };
+
   meta = with lib; {
     description = "Structural variant caller for mapped DNA sequenced data";
     license = licenses.bsd3;
     maintainers = with maintainers; [ scalavision ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
     longDescription = ''
       Delly is an integrated structural variant (SV) prediction method
       that can discover, genotype and visualize deletions, tandem duplications,

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 2/3] 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.
     '';
   };
-}
+})

From 7cec88e50f4cea409c13c05eed63ae6f9cd7839b Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Fri, 14 Jul 2023 00:20:20 +0900
Subject: [PATCH 3/3] delly: enable openmp

---
 pkgs/applications/science/biology/delly/default.nix | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix
index 2cde00036604..92eda1d1dd13 100644
--- a/pkgs/applications/science/biology/delly/default.nix
+++ b/pkgs/applications/science/biology/delly/default.nix
@@ -4,6 +4,7 @@
 , boost
 , bzip2
 , htslib
+, llvmPackages
 , xz
 , zlib
 , delly
@@ -27,10 +28,11 @@ stdenv.mkDerivation (finalAttrs: {
     htslib
     xz
     zlib
-  ];
+  ] ++ lib.optional stdenv.isDarwin llvmPackages.openmp;
 
   makeFlags = [
     "EBROOTHTSLIB=${htslib}"
+    "PARALLEL=1"
   ];
 
   installPhase = ''