diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology/somatic-sniper')
| -rw-r--r-- | nixpkgs/pkgs/applications/science/biology/somatic-sniper/default.nix | 30 | ||||
| -rw-r--r-- | nixpkgs/pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch | 26 |
2 files changed, 56 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/somatic-sniper/default.nix b/nixpkgs/pkgs/applications/science/biology/somatic-sniper/default.nix new file mode 100644 index 000000000000..553725fb4566 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/somatic-sniper/default.nix @@ -0,0 +1,30 @@ +{lib, stdenv, fetchFromGitHub, cmake, zlib, ncurses}: + +stdenv.mkDerivation rec { + pname = "somatic-sniper"; + version = "1.0.5.0"; + + src = fetchFromGitHub { + owner = "genome"; + repo = "somatic-sniper"; + rev = "v${version}"; + sha256 = "0lk7p9sp6mp50f6w1nppqhr40fcwy1asw06ivw8w8jvvnwaqf987"; + }; + + patches = [ ./somatic-sniper.patch ]; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ zlib ncurses ]; + + enableParallelBuilding = false; + + meta = with lib; { + description = "Identify single nucleotide positions that are different between tumor and normal"; + mainProgram = "bam-somaticsniper"; + license = licenses.mit; + homepage = "https://github.com/genome/somatic-sniper"; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.linux; + }; + +} diff --git a/nixpkgs/pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch b/nixpkgs/pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch new file mode 100644 index 000000000000..9af04c0a0696 --- /dev/null +++ b/nixpkgs/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 |