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| author | Justin Bedő <cu@cua0.org> | 2018-08-02 06:11:13 +1000 |
|---|---|---|
| committer | xeji <36407913+xeji@users.noreply.github.com> | 2018-08-01 22:11:13 +0200 |
| commit | 51fc0ef8d2f3b75bdd370a2d5380635115f92c03 (patch) | |
| tree | 616f06fb22757f073a3d4b4b8b59c5398e50cee1 | |
| parent | 383578689684bdfa47ef2b9c71e92439de5f3b50 (diff) | |
somatic-sniper: init 1.0.5.0 (#43403)
| -rw-r--r-- | pkgs/applications/science/biology/somatic-sniper/default.nix | 26 | ||||
| -rw-r--r-- | pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch | 26 | ||||
| -rw-r--r-- | pkgs/top-level/all-packages.nix | 2 |
3 files changed, 54 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/somatic-sniper/default.nix b/pkgs/applications/science/biology/somatic-sniper/default.nix new file mode 100644 index 0000000000000..adc8648c69809 --- /dev/null +++ b/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; + }; + +} diff --git a/pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch b/pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch new file mode 100644 index 0000000000000..9af04c0a0696d --- /dev/null +++ b/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 diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 8a95c387ab464..06c535f46c304 100644 --- a/pkgs/top-level/all-packages.nix +++ b/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 { }; |