somatic-sniper: init 1.0.5.0 (#43403)

pkgs/applications/science/biology/somatic-sniper/default.nix

@@ -0,0 +1,26 @@
+{stdenv, fetchFromGitHub, cmake, zlib, ncurses}:
+
+stdenv.mkDerivation rec {
+  name = "somatic-sniper-${version}";
+  version = "1.0.5.0";
+
+  src = fetchFromGitHub {
+    owner = "genome";
+    repo = "somatic-sniper";
+    rev = "v${version}";
+    sha256 = "0lk7p9sp6mp50f6w1nppqhr40fcwy1asw06ivw8w8jvvnwaqf987";
+  };
+
+  patches = [ ./somatic-sniper.patch ];
+
+  buildInputs = [ cmake zlib ncurses ];
+
+  meta = with stdenv.lib; {
+    description = "Identify single nucleotide positions that are different between tumor and normal";
+    license = licenses.mit;
+    homepage = https://github.com/genome/somatic-sniper;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.linux;
+  };
+
+}

pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch

@@ -0,0 +1,26 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 6d5a180..7254292 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -11,7 +11,7 @@ set(CMAKE_MODULE_PATH
+     )
+ 
+ include(TestHelper)
+-include(VersionHelper)
++#include(VersionHelper)
+ include(ProjectHelper)
+ 
+ # NOTE: for sniper we want the exe suffix to be like 0.7.4, not just 0.7
+diff --git a/vendor/samtools.patch b/vendor/samtools.patch
+index f173017..654f878 100644
+--- a/vendor/samtools.patch
++++ b/vendor/samtools.patch
+@@ -6,7 +6,7 @@ diff -Nuar a/Makefile b/Makefile
+  
+  samtools:lib $(AOBJS)
+ -		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam
+-+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -L. -lbam -lz
+++		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lncurses -L. -lbam -lz
+  
+  razip:razip.o razf.o
+  		$(CC) $(CFLAGS) -o $@ razf.o razip.o -lz

pkgs/top-level/all-packages.nix

@@ -20426,6 +20426,8 @@ with pkgs;
 
   snpeff = callPackage ../applications/science/biology/snpeff { };
 
+  somatic-sniper = callPackage ../applications/science/biology/somatic-sniper { };
+
   star = callPackage ../applications/science/biology/star { };
 
   varscan = callPackage ../applications/science/biology/varscan { };