bwa-mem2: fix compilation isssue

On latest unstable, there are several implicit function declaration.
in safestrlib, which was not a seperate package but simply a submodule.

It is now a separate package (see previous commit) and using latest
unstable for this libary fixes the issue.

pkgs/by-name/bw/bwa-mem2/no-submodule.patch

@@ -0,0 +1,42 @@
+diff --git a/Makefile b/Makefile
+index 359585f..13ec279 100644
+--- a/Makefile
++++ b/Makefile
+@@ -49,7 +49,6 @@ OBJS=		src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.
+ 			src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o \
+ 			src/bwamem_extra.o src/kopen.o
+ BWA_LIB=    libbwa.a
+-SAFE_STR_LIB=    ext/safestringlib/libsafestring.a
+ 
+ ifeq ($(arch),sse41)
+ 	ifeq ($(CXX), icpc)
+@@ -101,16 +100,6 @@ CXXFLAGS+=	-g -O3 -fpermissive $(ARCH_FLAGS) #-Wall ##-xSSE2
+ all:$(EXE)
+ 
+ multi:
+-	rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
+-	$(MAKE) arch=sse41    EXE=bwa-mem2.sse41    CXX=$(CXX) all
+-	rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
+-	$(MAKE) arch=sse42    EXE=bwa-mem2.sse42    CXX=$(CXX) all
+-	rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
+-	$(MAKE) arch=avx    EXE=bwa-mem2.avx    CXX=$(CXX) all
+-	rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
+-	$(MAKE) arch=avx2   EXE=bwa-mem2.avx2     CXX=$(CXX) all
+-	rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean;
+-	$(MAKE) arch=avx512 EXE=bwa-mem2.avx512bw CXX=$(CXX) all
+ 	$(CXX) -Wall -O3 src/runsimd.cpp -Iext/safestringlib/include -Lext/safestringlib/ -lsafestring $(STATIC_GCC) -o bwa-mem2
+ 
+ 
+@@ -120,12 +109,8 @@ $(EXE):$(BWA_LIB) $(SAFE_STR_LIB) src/main.o
+ $(BWA_LIB):$(OBJS)
+ 	ar rcs $(BWA_LIB) $(OBJS)
+ 
+-$(SAFE_STR_LIB):
+-	cd ext/safestringlib/ && $(MAKE) clean && $(MAKE) CC=$(CC) directories libsafestring.a
+-
+ clean:
+ 	rm -fr src/*.o $(BWA_LIB) $(EXE) bwa-mem2.sse41 bwa-mem2.sse42 bwa-mem2.avx bwa-mem2.avx2 bwa-mem2.avx512bw
+-	cd ext/safestringlib/ && $(MAKE) clean
+ 
+ depend:
+ 	(LC_ALL=C; export LC_ALL; makedepend -Y -- $(CXXFLAGS) $(CPPFLAGS) -I. -- src/*.cpp)

pkgs/by-name/bw/bwa-mem2/package.nix

@@ -2,6 +2,7 @@
   lib,
   stdenv,
   fetchFromGitHub,
+  safestringlib,
   zlib,
 }:
 
@@ -13,21 +14,11 @@ stdenv.mkDerivation (finalAttrs: {
     owner = "bwa-mem2";
     repo = "bwa-mem2";
     rev = "cf4306a47dac35e7e79a9e75398a35f33900cfd0";
-    fetchSubmodules = true;
+    hash = "sha256-hY8nLRFWt0GAElhDIcYdUX6cJrzOE3NlYRQr0tC3on4=";
-    hash = "sha256-1AYSn7nBrDwbX7oSrdEoa1d3t6xzwKnA0S87Y/XeXJg=";
   };
 
   buildInputs = [ zlib ];
 
-  # see https://github.com/bwa-mem2/bwa-mem2/issues/93
-  postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
-    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/include/safe_mem_lib.h
-    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset16_s.c
-    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset32_s.c
-    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset_s.c
-    sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/wmemset_s.c
-  '';
-
   buildFlags = [
     (
       if stdenv.hostPlatform.sse4_2Support then
@@ -43,14 +34,45 @@ stdenv.mkDerivation (finalAttrs: {
     )
   ];
 
-  env = lib.optionalAttrs stdenv.hostPlatform.isDarwin {
+  patches = [
-    NIX_CFLAGS_COMPILE = toString [
+    ./no-submodule.patch
+  ];
+
+  # Also, patch the tests
+  postPatch =
+    # Force path to static link, otherwise, it fails at runtime to
+    # find the shared library
+    ''
+      substituteInPlace Makefile \
+        --replace-fail "-Iext/safestringlib/include" "-I${safestringlib}/include" \
+        --replace-fail "-Lext/safestringlib" "-L${safestringlib}/lib"
+    ''
+    # Make test compile by changing the compiler and path to library
+    # Remove xeonbsw test that fails to compile due to missing _rdsc
+    # also, not portable
+    + ''
+      substituteInPlace test/Makefile \
+        --replace-fail "icpc" "g++" \
+        --replace-fail "../ext/safestringlib/libsafestring.a"  \
+                       "${safestringlib}/lib/libsafestring.a" \
+        --replace-fail \
+          "fmi_test smem2_test bwt_seed_strategy_test sa2ref_test xeonbsw" \
+          "fmi_test smem2_test bwt_seed_strategy_test sa2ref_test"
+    '';
+
+  env.NIX_CFLAGS_COMPILE = toString (
+    lib.optionals stdenv.hostPlatform.isDarwin [
       "-Wno-error=register"
       "-Wno-error=implicit-function-declaration"
-    ];
+    ]
-  };
+  );
+
+  nativeBuildInputs = [
+    safestringlib
+  ];
 
   enableParallelBuilding = true;
+
   installPhase = ''
     runHook preInstall