From a92211886b1987a8a70791f3f6f37e56857b104c Mon Sep 17 00:00:00 2001
From: Sergei Trofimovich <slyich@gmail.com>
Date: Wed, 29 Dec 2021 17:05:24 +0000
Subject: strelka: fix build on gcc-12

Without the change build fails as:

    src/c++/lib/calibration/IndelErrorModel.hh:100:33: error: 'numeric_limits' is not a member of 'std'
      100 |     double logErrorRate = -std::numeric_limits<double>::infinity();
          |                                 ^~~~~~~~~~~~~~
---
 pkgs/applications/science/biology/strelka/default.nix | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

(limited to 'pkgs/applications/science')

diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix
index 9730601e4e7d..c66afa150c86 100644
--- a/pkgs/applications/science/biology/strelka/default.nix
+++ b/pkgs/applications/science/biology/strelka/default.nix
@@ -1,4 +1,4 @@
-{lib, stdenv, fetchFromGitHub, cmake, zlib, python2}:
+{lib, stdenv, fetchFromGitHub, fetchpatch, cmake, zlib, python2}:
 
 stdenv.mkDerivation rec {
   pname = "strelka";
@@ -11,6 +11,16 @@ stdenv.mkDerivation rec {
     sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf";
   };
 
+  patches = [
+    # Pull pending fix for gcc-12:
+    #   https://github.com/Illumina/strelka/pull/204
+    (fetchpatch {
+      name = "limits.patch";
+      url = "https://github.com/Illumina/strelka/commit/98272cd345c6e4c672e6a5b7721204fcac0502d6.patch";
+      hash = "sha256-psBiuN32nvwZ+QX51JQjIdRhEE3k7PfwbkD10ckqvZk=";
+    })
+  ];
+
   nativeBuildInputs = [ cmake ];
   buildInputs = [ zlib python2 ];
 
-- 
cgit 1.4.1


From 3ce2a25e504a72e727e6bdf845655344e55ee4a6 Mon Sep 17 00:00:00 2001
From: Weijia Wang <9713184+wegank@users.noreply.github.com>
Date: Mon, 11 Dec 2023 13:37:17 +0100
Subject: strelka: add aarch64-linux support

---
 pkgs/applications/science/biology/strelka/default.nix | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

(limited to 'pkgs/applications/science')

diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix
index c66afa150c86..ad6c0d9e5a4c 100644
--- a/pkgs/applications/science/biology/strelka/default.nix
+++ b/pkgs/applications/science/biology/strelka/default.nix
@@ -1,4 +1,4 @@
-{lib, stdenv, fetchFromGitHub, fetchpatch, cmake, zlib, python2}:
+{lib, stdenv, fetchFromGitHub, fetchpatch, cmake, boost, zlib, python2}:
 
 stdenv.mkDerivation rec {
   pname = "strelka";
@@ -21,8 +21,18 @@ stdenv.mkDerivation rec {
     })
   ];
 
+  postPatch = ''
+    substituteInPlace src/cmake/boost.cmake \
+      --replace "1.58.0" "${boost.version}" \
+      --replace "Boost_USE_STATIC_LIBS ON" "Boost_USE_STATIC_LIBS OFF"
+  '';
+
   nativeBuildInputs = [ cmake ];
-  buildInputs = [ zlib python2 ];
+  buildInputs = [ boost zlib python2 ];
+
+  cmakeFlags = [
+    "-DCMAKE_CXX_STANDARD=14"
+  ];
 
   env.NIX_CFLAGS_COMPILE = toString [
     "-Wno-error=maybe-uninitialized"
@@ -47,7 +57,7 @@ stdenv.mkDerivation rec {
     license = licenses.gpl3;
     homepage = "https://github.com/Illumina/strelka";
     maintainers = with maintainers; [ jbedo ];
-    platforms = [ "x86_64-linux" ];
+    platforms = platforms.linux;
   };
 
 }
-- 
cgit 1.4.1