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somatic-sniper: init 1.0.5.0 (#43403)

nixos-19.03
Justin Bedő 4 years ago
committed by xeji
parent
commit
51fc0ef8d2
  1. 26
      pkgs/applications/science/biology/somatic-sniper/default.nix
  2. 26
      pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch
  3. 2
      pkgs/top-level/all-packages.nix

26
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;
};
}

26
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

2
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 { };

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