Merge remote-tracking branch 'nixpkgs/nixos-unstable'

21 files changed, 141 insertions, 40 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix
index f4e2db01fbc5..46d39c1a7ba3 100644
--- a/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, python, bash }:
+{ lib, stdenv, fetchurl, htslib, zlib, bzip2, xz, curl, perl, python3, bash }:
 
 stdenv.mkDerivation rec {
   pname = "bcftools";
@@ -9,12 +9,19 @@ stdenv.mkDerivation rec {
     sha256 = "0r508mp15pqzf8r1269kb4v5naw9zsvbwd3cz8s1yj7carsf9viw";
   };
 
-  buildInputs = [ htslib zlib bzip2 lzma curl perl python ];
+  nativeBuildInputs = [
+    perl
+    python3
+  ];
+
+  buildInputs = [ htslib zlib bzip2 xz curl ];
+
+  strictDeps = true;
 
   makeFlags = [
     "HSTDIR=${htslib}"
     "prefix=$(out)"
-    "CC=cc"
+    "CC=${stdenv.cc.targetPrefix}cc"
   ];
 
   preCheck = ''
diff --git a/nixpkgs/pkgs/applications/science/biology/bedops/default.nix b/nixpkgs/pkgs/applications/science/biology/bedops/default.nix
new file mode 100644
index 000000000000..407ed0c01f76
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/bedops/default.nix
@@ -0,0 +1,51 @@
+{ lib, stdenv, fetchFromGitHub, zlib, bzip2, jansson, makeWrapper }:
+
+stdenv.mkDerivation rec {
+  pname = "bedops";
+  version = "2.4.39";
+
+  src = fetchFromGitHub {
+    owner = "bedops";
+    repo = "bedops";
+    rev = "v${version}";
+    sha256 = "sha256-vPrut3uhZK1Eg9vPcyxVNWW4zKeypdsb28oM1xbbpJo=";
+  };
+
+  buildInputs = [ zlib bzip2 jansson ];
+  nativeBuildInputs = [ makeWrapper ];
+
+  preConfigure = ''
+    # We use nixpkgs versions of these libraries
+    rm -r third-party
+    sed -i '/^LIBS/d' system.mk/*
+    sed -i 's|^LIBRARIES.*$|LIBRARIES = -lbz2 -lz -ljansson|' */*/*/*/Makefile
+    substituteInPlace applications/bed/starch/src/Makefile --replace '$(LIBRARIES)' ""
+
+    # Function name is different in nixpkgs provided libraries
+    for f in interfaces/src/data/starch/starchFileHelpers.c applications/bed/starch/src/starchcat.c ; do
+      substituteInPlace $f --replace deflateInit2cpp deflateInit2
+    done
+
+    # Don't force static
+    for f in */*/*/*/Makefile ; do
+      substituteInPlace $f --replace '-static' ""
+    done
+  '';
+
+  makeFlags = [ "BINDIR=$(out)/bin" ];
+
+  postFixup = ''
+    for f in $out/bin/* ; do
+      wrapProgram $f --prefix PATH : "$out/bin"
+    done
+  '';
+
+  meta = with lib; {
+    description = "Suite of tools for addressing questions arising in genomics studies";
+    homepage = "https://github.com/bedops/bedops";
+    license = licenses.gpl2Only;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.x86_64;
+    broken = stdenv.isDarwin;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
index d0553bb0649a..aac36d2af310 100644
--- a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
@@ -1,4 +1,4 @@
-{lib, stdenv, fetchFromGitHub, zlib, python, bzip2, lzma}:
+{lib, stdenv, fetchFromGitHub, zlib, python3, bzip2, xz}:
 
 stdenv.mkDerivation rec {
   pname = "bedtools";
@@ -11,7 +11,14 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-NqKldF7ePJn3pT+AkESIQghBKSFFOEBBsTaKEbU+oaQ=";
   };
 
-  buildInputs = [ zlib python bzip2 lzma ];
+  strictDeps = true;
+
+  nativeBuildInputs = [
+    python3
+  ];
+
+  buildInputs = [ zlib bzip2 xz ];
+
   cxx = if stdenv.cc.isClang then "clang++" else "g++";
   cc = if stdenv.cc.isClang then "clang" else "gcc";
   buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} -j $NIX_BUILD_CORES";
diff --git a/nixpkgs/pkgs/applications/science/biology/delly/default.nix b/nixpkgs/pkgs/applications/science/biology/delly/default.nix
index efaa4403f41d..fe81ff44d245 100644
--- a/nixpkgs/pkgs/applications/science/biology/delly/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/delly/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchpatch, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }:
+{ lib, stdenv, fetchpatch, fetchFromGitHub, htslib, zlib, bzip2, xz, ncurses, boost }:
 
 stdenv.mkDerivation rec {
   pname = "delly";
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
       sha256 = "sha256-DWwC35r8cQbePUzppkFQlev0YZdxk2+BSrNTW/DOY3M=";
   };
 
-  buildInputs = [ zlib htslib bzip2 lzma ncurses boost ];
+  buildInputs = [ zlib htslib bzip2 xz ncurses boost ];
 
   EBROOTHTSLIB = htslib;
 
diff --git a/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix b/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix
index 7eb3afd437af..b42fed8da281 100644
--- a/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix
@@ -16,7 +16,7 @@ python27Packages.buildPythonApplication rec {
     sha256 = "0abnmn0bh11jihf5d3cggiild1ykawzv5f5fhb4cyyi8fvy4hcxf";
   });
 
-  buildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
   propagatedBuildInputs = [ python27Packages.biopython wget diamond hmmer ];
 
   # make emapper find diamond & hmmer
diff --git a/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix b/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix
index 32ab614b9682..8646b8ca54a8 100644
--- a/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, zlib, bzip2, lzma }:
+{ lib, stdenv, fetchFromGitHub, zlib, bzip2, xz }:
 
 stdenv.mkDerivation rec {
   pname = "freebayes";
@@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
     fetchSubmodules = true;
   };
 
-  buildInputs = [ zlib bzip2 lzma ];
+  buildInputs = [ zlib bzip2 xz ];
 
   installPhase = ''
     install -vD bin/freebayes bin/bamleftalign scripts/* -t $out/bin
diff --git a/nixpkgs/pkgs/applications/science/biology/kent/default.nix b/nixpkgs/pkgs/applications/science/biology/kent/default.nix
index 26c55d3dc383..12bbfa09c251 100644
--- a/nixpkgs/pkgs/applications/science/biology/kent/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/kent/default.nix
@@ -3,7 +3,7 @@
 , libuuid
 , zlib
 , bzip2
-, lzma
+, xz
 , openssl
 , curl
 , libmysqlclient
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
     sha256 = "0l5lmqqc6sqkf4hyk3z4825ly0vdlj5xdfad6zd0708cb1v81nbx";
   };
 
-  buildInputs = [ libpng libuuid zlib bzip2 lzma openssl curl libmysqlclient ];
+  buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ];
 
   patchPhase = ''
     substituteInPlace ./src/checkUmask.sh \
diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix
index 3a36a2194a13..0c5b81452fd5 100644
--- a/nixpkgs/pkgs/applications/science/biology/last/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/last/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "last";
-  version = "1170";
+  version = "1179";
 
   src = fetchurl {
     url = "http://last.cbrc.jp/last-${version}.zip";
-    sha256 = "sha256-hBuG6QGXtBrvNrtaZU+i8gxu2ZQw+srFRkbuWoL5JHc=";
+    sha256 = "sha256-949oiE7ZNkCOJuOK/huPkCN0c4TlVaTskkBe0joc0HU=";
   };
 
   nativeBuildInputs = [ unzip ];
diff --git a/nixpkgs/pkgs/applications/science/biology/meme-suite/default.nix b/nixpkgs/pkgs/applications/science/biology/meme-suite/default.nix
new file mode 100644
index 000000000000..bfa561437e74
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/meme-suite/default.nix
@@ -0,0 +1,21 @@
+{ lib, stdenv, fetchurl, python3, perl, glibc, zlib }:
+
+stdenv.mkDerivation rec {
+  pname = "meme-suite";
+  version = "5.1.1";
+
+  src = fetchurl {
+    url = "https://meme-suite.org/meme-software/${version}/meme-${version}.tar.gz";
+    sha256 = "38d73d256d431ad4eb7da2c817ce56ff2b4e26c39387ff0d6ada088938b38eb5";
+  };
+
+  buildInputs = [ zlib ];
+  nativeBuildInputs = [ perl python3 ];
+
+  meta = with lib; {
+    description = "Motif-based sequence analysis tools";
+    license = licenses.unfree;
+    maintainers = with maintainers; [ gschwartz ];
+    platforms = platforms.linux;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix b/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix
index 687a2a985f28..9d9e46bc7800 100644
--- a/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix
@@ -1,12 +1,12 @@
 { lib, stdenv, fetchurl, cmake, gcc, gcc-unwrapped }:
 
 stdenv.mkDerivation rec {
-  version = "3.2.1";
+  version = "3.6";
   pname = "messer-slim";
 
   src = fetchurl {
     url = "https://github.com/MesserLab/SLiM/archive/v${version}.tar.gz";
-    sha256 = "1j3ssjvxpsc21mmzj59kwimglz8pdazi5w6wplmx11x744k77wa1";
+    sha256 = "sha256-djWUKB+NW2a/6oaAMcH0Ul/R/XPHvGDbwlfeFmkbMOY=";
   };
 
   nativeBuildInputs = [ cmake gcc gcc-unwrapped ];
diff --git a/nixpkgs/pkgs/applications/science/biology/octopus/default.nix b/nixpkgs/pkgs/applications/science/biology/octopus/default.nix
index b7a4a4c1a2a0..0ef48ec6413b 100644
--- a/nixpkgs/pkgs/applications/science/biology/octopus/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/octopus/default.nix
@@ -1,18 +1,30 @@
-{lib, stdenv, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, lzma, pkg-config}:
+{lib, stdenv, fetchpatch, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, xz, pkg-config}:
 
 stdenv.mkDerivation rec {
   pname = "octopus";
-  version = "0.7.0";
+  version = "0.7.1";
 
   src = fetchFromGitHub {
     owner = "luntergroup";
     repo = "octopus";
     rev = "v${version}";
-    sha256 = "0y3g0xc3x3adbcmds6hh60023pfv1qrz6ak7jd88fg9vxi9bdrfb";
+    sha256 = "sha256-TZ57uKTZ87FWpLNGPY8kbML1EDM8fnEFbXR+Z3dmiao=";
   };
 
+  patches = [
+    # Backport TZ patchs (https://github.com/luntergroup/octopus/issues/149)
+    (fetchpatch {
+      url = "https://github.com/luntergroup/octopus/commit/3dbd8cc33616129ad356e99a4dae82e4f6702250.patch";
+      sha256 = "sha256-UCufVU9x+L1zCEhkr/48KFYRvh8w26w8Jr+O+wULKK8=";
+    })
+    (fetchpatch {
+      url = "https://github.com/luntergroup/octopus/commit/af5a66a2792bd098fb53eb79fb4822625f09305e.patch";
+      sha256 = "sha256-r8jv6EZHfTWVLYUBau3F+ilOd9IeH8rmatorEY5LXP4=";
+    })
+  ];
+
   nativeBuildInputs = [ cmake pkg-config ];
-  buildInputs = [ boost gmp htslib zlib lzma ];
+  buildInputs = [ boost gmp htslib zlib xz ];
 
   postInstall = ''
     mkdir $out/bin
diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
index 52a17e8d01cd..ed0d043cd542 100644
--- a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "picard-tools";
-  version = "2.25.0";
+  version = "2.25.1";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "sha256-+vJDTahP4htRbVeBd2eSD97fwZ69wB2cro1tMxT36Jc=";
+    sha256 = "sha256-bW5iLWtGX5/HBMN7y6VbDaxa0U0HCIu9vfreXNAn7hw=";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/nixpkgs/pkgs/applications/science/biology/platypus/default.nix b/nixpkgs/pkgs/applications/science/biology/platypus/default.nix
index 30bc68fb0e87..d602395b8757 100644
--- a/nixpkgs/pkgs/applications/science/biology/platypus/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/platypus/default.nix
@@ -13,7 +13,8 @@ in stdenv.mkDerivation {
     sha256 = "0nah6r54b8xm778gqyb8b7rsd76z8ji4g73sm6rvpw5s96iib1vw";
   };
 
-  buildInputs = [ htslib python zlib makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ htslib python zlib ];
 
   buildPhase = ''
     patchShebangs .
diff --git a/nixpkgs/pkgs/applications/science/biology/prodigal/default.nix b/nixpkgs/pkgs/applications/science/biology/prodigal/default.nix
index 22883cc522f1..28a21522c6b8 100644
--- a/nixpkgs/pkgs/applications/science/biology/prodigal/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/prodigal/default.nix
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
   };
 
   makeFlags = [
-    "CC=cc"
+    "CC=${stdenv.cc.targetPrefix}cc"
     "INSTALLDIR=$(out)/bin"
   ];
 
diff --git a/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix b/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix
index 8802736efac8..7b5141302f7b 100644
--- a/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix
@@ -1,18 +1,18 @@
-{ lib, stdenv, fetchFromGitHub, python3, which, dmd, ldc, zlib }:
+{ lib, stdenv, fetchFromGitHub, python3, which, ldc, zlib }:
 
 stdenv.mkDerivation rec {
   pname = "sambamba";
-  version = "0.7.1";
+  version = "0.8.0";
 
   src = fetchFromGitHub {
     owner = "biod";
     repo = "sambamba";
     rev = "v${version}";
-    sha256 = "0k5wy06zrbsc40x6answgz7rz2phadyqwlhi9nqxbfqanbg9kq20";
+    sha256 = "sha256:0kx5a0fmvv9ldz2hnh7qavgf7711kqc73zxf51k4cca4hr58zxr9";
     fetchSubmodules = true;
   };
 
-  nativeBuildInputs = [ which python3 dmd ldc ];
+  nativeBuildInputs = [ which python3 ldc ];
   buildInputs = [ zlib ];
 
   # Upstream's install target is broken; copy manually
diff --git a/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix b/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix
index 32701af8392c..4c32516b29f6 100644
--- a/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0i12mv93bfv8xjwc3rs2x73d6hkvi7kgbbbx3ry984l3ly4p6nnm";
   };
 
-  buildInputs = [ unzip jre makeWrapper ];
+  nativeBuildInputs = [ makeWrapper unzip ];
+  buildInputs = [ jre ];
 
   sourceRoot = "snpEff";
 
diff --git a/nixpkgs/pkgs/applications/science/biology/spades/default.nix b/nixpkgs/pkgs/applications/science/biology/spades/default.nix
index ec381693aedf..e6f33d6cde90 100644
--- a/nixpkgs/pkgs/applications/science/biology/spades/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/spades/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "SPAdes";
-  version = "3.14.1";
+  version = "3.15.2";
 
   src = fetchurl {
     url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz";
-    sha256 = "1ji3afn6yvx7ysg7p9j0d1g28zrnxg1b7x90mhs2bj3lgs7vfafn";
+    sha256 = "03cxz4m1n4rc81lqb4p1pz2ammms7f31wvi4daywfkc13aal6fz9";
   };
 
   nativeBuildInputs = [ cmake ];
@@ -19,9 +19,9 @@ stdenv.mkDerivation rec {
 
   meta = with lib; {
     description = "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines";
-    license = licenses.gpl2;
+    license = licenses.gpl2Only;
     homepage = "http://cab.spbu.ru/software/spades/";
-    platforms = platforms.unix;
+    platforms = with platforms; [ "x86_64-linux" "x86_64-darwin"];
     maintainers = [ maintainers.bzizou ];
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
index c208d80d5769..16091514f154 100644
--- a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
@@ -2,10 +2,10 @@
 
 stdenv.mkDerivation rec {
   pname = "stacks";
-  version = "2.53";
+  version = "2.55";
   src = fetchurl {
     url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz";
-    sha256 = "1zchds205nwdqch1246953dr8c0019yas178qbq3jypbxvmgq7pf";
+    sha256 = "sha256-p8L0F3A+GdNsPgTQNn9Em5EjFCc9f7gUvyLIRCTd05c=";
   };
 
   buildInputs = [ zlib ];
diff --git a/nixpkgs/pkgs/applications/science/biology/star/default.nix b/nixpkgs/pkgs/applications/science/biology/star/default.nix
index 345863847377..9ad53502cd76 100644
--- a/nixpkgs/pkgs/applications/science/biology/star/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/star/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "star";
-  version = "2.7.7a";
+  version = "2.7.8a";
 
   src = fetchFromGitHub {
     repo = "STAR";
     owner = "alexdobin";
     rev = version;
-    sha256 = "sha256-0K49yjcnTzC56ZIB20OeTiMJ5EW8mRx+xEpyWEfFcts=";
+    sha256 = "sha256-2qqdCan67bcoUGgr5ro2LGGHDAyS/egTrT8pWX1chX0=";
   };
 
   sourceRoot = "source/source";
diff --git a/nixpkgs/pkgs/applications/science/biology/svaba/default.nix b/nixpkgs/pkgs/applications/science/biology/svaba/default.nix
index 87b77f6ac045..1aed501919f9 100644
--- a/nixpkgs/pkgs/applications/science/biology/svaba/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/svaba/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, zlib, bzip2, lzma, fetchFromGitHub } :
+{ lib, stdenv, zlib, bzip2, xz, fetchFromGitHub } :
 
 stdenv.mkDerivation rec {
   version = "1.1.0";
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
     fetchSubmodules = true;
   };
 
-  buildInputs = [ zlib bzip2 lzma ];
+  buildInputs = [ zlib bzip2 xz ];
 
   installPhase = ''
     runHook preInstall
diff --git a/nixpkgs/pkgs/applications/science/biology/varscan/default.nix b/nixpkgs/pkgs/applications/science/biology/varscan/default.nix
index 65a19b83a70e..2a232d64693d 100644
--- a/nixpkgs/pkgs/applications/science/biology/varscan/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/varscan/default.nix
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-+yO3KrZ2+1qJvQIJHCtsmv8hC5a+4E2d7mrvTYtygU0=";
   };
 
-  buildInputs = [ jre makeWrapper ];
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ jre ];
 
   phases = [ "installPhase" ];