Merge remote-tracking branch 'upstream/master' into gcc-8

13 files changed, 89 insertions, 25 deletions

diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix
index 406f42e9ad7b..2cdd7fda38ef 100644
--- a/pkgs/applications/science/biology/bedtools/default.nix
+++ b/pkgs/applications/science/biology/bedtools/default.nix
@@ -1,17 +1,17 @@
-{stdenv, fetchFromGitHub, zlib, python}:
+{stdenv, fetchFromGitHub, zlib, python, bzip2, lzma}:
 
 stdenv.mkDerivation rec {
   name = "bedtools-${version}";
-  version = "2.27.1";
+  version = "2.28.0";
 
   src = fetchFromGitHub {
     owner = "arq5x";
     repo = "bedtools2";
     rev = "v${version}";
-    sha256 = "1pk68y052rm2m24yfmy82ms8p6kd6xcqxxgi7n0a1sbh89wllm6s";
+    sha256 = "1266bcn5hgbvysfi6nr4cqxlbxcx7vn7ng8kb0v3gz37qh2zxxw9";
   };
 
-  buildInputs = [ zlib python ];
+  buildInputs = [ zlib python bzip2 lzma ];
   cc = if stdenv.cc.isClang then "clang++" else "g++";
   buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} -j $NIX_BUILD_CORES";
   installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} install";
diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix
index 781ceb3df59e..0e2b5d8b25fe 100644
--- a/pkgs/applications/science/biology/dcm2niix/default.nix
+++ b/pkgs/applications/science/biology/dcm2niix/default.nix
@@ -2,21 +2,22 @@
 , fetchFromGitHub
 , cmake
 , libyamlcpp
+, git
 }:
 
 stdenv.mkDerivation rec {
-  version = "1.0.20170130";
+  version = "1.0.20190410";
   name = "dcm2niix-${version}";
 
   src = fetchFromGitHub {
     owner = "rordenlab";
     repo = "dcm2niix";
     rev = "v${version}";
-    sha256 = "1f2nzd8flp1rfn725bi64z7aw3ccxyyygzarxijw6pvgl476i532";
+    sha256 = "1prwpvbi76xlpkhc4kadjhyyx0s71cs30hi6anknhfm6hdyd26ms";
   };
 
   enableParallelBuilding = true;
-  nativeBuildInputs = [ cmake ];
+  nativeBuildInputs = [ cmake git ];
   buildInputs = [ libyamlcpp ];
 
   meta = with stdenv.lib; {
diff --git a/pkgs/applications/science/biology/est-sfs/default.nix b/pkgs/applications/science/biology/est-sfs/default.nix
new file mode 100644
index 000000000000..dcc725233551
--- /dev/null
+++ b/pkgs/applications/science/biology/est-sfs/default.nix
@@ -0,0 +1,28 @@
+{ stdenv, fetchurl, gsl }:
+
+stdenv.mkDerivation rec {
+  pname = "est-sfs";
+  version = "2.03";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/est-usfs/${pname}-release-${version}.tar.gz";
+    sha256 = "1hvamrgagz0xi89w8qafyd9mjrdpyika8zm22drddnjkp4sdj65n";
+  };
+
+  buildInputs = [ gsl ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    mkdir -p $out/share/doc/${pname}
+    cp est-sfs $out/bin
+    cp est-sfs-documentation.pdf $out/share/doc/${pname}
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://sourceforge.net/projects/est-usfs;
+    description = "Estimate the unfolded site frequency spectrum and ancestral states";
+    license = licenses.gpl3;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/applications/science/biology/hisat2/default.nix b/pkgs/applications/science/biology/hisat2/default.nix
index 9ccf54a81133..9d41fed06911 100644
--- a/pkgs/applications/science/biology/hisat2/default.nix
+++ b/pkgs/applications/science/biology/hisat2/default.nix
@@ -1,4 +1,4 @@
-{stdenv, fetchurl, unzip, which, python}:
+{stdenv, fetchurl, unzip, which, python, perl}:
 
 stdenv.mkDerivation rec {
   name = "hisat2-${version}";
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "10g73sdf6vqqfhhd92hliw7bbpkb8v4pp5012r5l21zws7p7d8l9";
   };
 
-  buildInputs = [ unzip  which python ];
+  nativeBuildInputs = [ unzip which ];
+  buildInputs = [ python perl ];
 
   installPhase = ''
     mkdir -p $out/bin
diff --git a/pkgs/applications/science/biology/itsx/default.nix b/pkgs/applications/science/biology/itsx/default.nix
index 804e71c1bfa7..0c8c7313bf2a 100644
--- a/pkgs/applications/science/biology/itsx/default.nix
+++ b/pkgs/applications/science/biology/itsx/default.nix
@@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing";
-    homepage = http://microbiology.se/software/itsx/;
+    homepage = https://microbiology.se/software/itsx/;
     license = licenses.gpl3;
     maintainers = [ maintainers.bzizou ];
     platforms = [ "x86_64-linux" "i686-linux" ];
diff --git a/pkgs/applications/science/biology/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix
index 3cd83a5cdd27..1bdb31616e4d 100644
--- a/pkgs/applications/science/biology/mosdepth/default.nix
+++ b/pkgs/applications/science/biology/mosdepth/default.nix
@@ -4,26 +4,26 @@ let
   hts-nim = fetchFromGitHub {
     owner = "brentp";
     repo = "hts-nim";
-    rev = "v0.2.5";
-    sha256 = "1fma99rjqxgg9dihkd10hm1jjp5amsk5wsxnvq1lk4mcsjix5xqb";
+    rev = "v0.2.14";
+    sha256 = "0d1z4b6mrppmz3hgkxd4wcy79w68icvhi7q7n3m2k17n8f3xbdx3";
   };
 
   docopt = fetchFromGitHub {
     owner = "docopt";
     repo = "docopt.nim";
-    rev = "v0.6.5";
-    sha256 = "0yx79m4jkdcazwlky55nwf39zj5kdhymrrdrjq29mahiwx83x5zr";
+    rev = "v0.6.7";
+    sha256 = "1ga7ckg21fzwwvh26jp2phn2h3pvkn8g8sm13dxif33rp471bv37";
   };
 
 in stdenv.mkDerivation rec {
   name = "mosdepth-${version}";
-  version = "0.2.3";
+  version = "0.2.6";
 
   src = fetchFromGitHub {
     owner = "brentp";
     repo = "mosdepth";
     rev = "v${version}";
-    sha256 = "1b9frrwhcvay3alhn0d02jccc2qlbij1732hzq9nhwnr4kvsvxx7";
+    sha256 = "0i9pl9lsli3y84ygxanrr525gfg8fs9h481944cbzsmqmbldwvgk";
   };
 
   buildInputs = [ nim ];
diff --git a/pkgs/applications/science/biology/niftyreg/default.nix b/pkgs/applications/science/biology/niftyreg/default.nix
index 9f24046b3bf6..9f1cb8db43d5 100644
--- a/pkgs/applications/science/biology/niftyreg/default.nix
+++ b/pkgs/applications/science/biology/niftyreg/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchurl, cmake, zlib }:
+{ stdenv, fetchurl, cmake, zlib }:
 
 stdenv.mkDerivation rec {
   pname   = "niftyreg";
diff --git a/pkgs/applications/science/biology/niftyseg/default.nix b/pkgs/applications/science/biology/niftyseg/default.nix
index 671ee4b95c65..e7221855503c 100644
--- a/pkgs/applications/science/biology/niftyseg/default.nix
+++ b/pkgs/applications/science/biology/niftyseg/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchurl, cmake, eigen, zlib }:
+{ stdenv, fetchurl, cmake, eigen, zlib }:
 
 stdenv.mkDerivation rec {
   pname   = "niftyseg";
diff --git a/pkgs/applications/science/biology/octopus/default.nix b/pkgs/applications/science/biology/octopus/default.nix
new file mode 100644
index 000000000000..0a2074a06e97
--- /dev/null
+++ b/pkgs/applications/science/biology/octopus/default.nix
@@ -0,0 +1,30 @@
+{stdenv, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, lzma, pkg-config}:
+
+stdenv.mkDerivation rec {
+  pname = "octopus";
+  version = "0.6.3-beta";
+  name = "${pname}-${version}";
+
+  src = fetchFromGitHub {
+    owner = "luntergroup";
+    repo = "octopus";
+    rev = "v${version}";
+    sha256 = "042fycg8ppld7iajpzq2d8h8wr0nw43zbl57y125sfihryvr373n";
+  };
+
+  nativeBuildInputs = [ cmake pkg-config ];
+  buildInputs = [ boost gmp htslib zlib lzma ];
+
+  postInstall = ''
+    mkdir $out/bin
+    mv $out/octopus $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Bayesian haplotype-based mutation calling";
+    license = licenses.mit;
+    homepage = "https://github.com/luntergroup/octopus";
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.x86_64;
+  };
+}
diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix
index 5fc222bb2993..e6a5ab741d94 100644
--- a/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "picard-tools-${version}";
-  version = "2.20.2";
+  version = "2.20.5";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "0qpc6pi3fmzv8rs5cmk3dd4clrkzbrngsl384b5g0y7471lhavbi";
+    sha256 = "107zlvp74ahpn652nfkipp80bbzf3fp812pi1ma42njk4wchah10";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/applications/science/biology/stacks/default.nix b/pkgs/applications/science/biology/stacks/default.nix
index d188ca02b183..e778c3bd52cc 100644
--- a/pkgs/applications/science/biology/stacks/default.nix
+++ b/pkgs/applications/science/biology/stacks/default.nix
@@ -2,10 +2,10 @@
     
 stdenv.mkDerivation rec {
   pname = "stacks";
-  version = "2.4";
+  version = "2.41";
   src = fetchurl {
     url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz";
-    sha256 = "1ha1avkh6rqqvsy4k42336a2gj14y1jq19a2x8cjmiidi9l3s29h";
+    sha256 = "0q420rzjb05jfchcls3pysm4hxfgs6xj2jw246isx0il10g93gkq";
   };
 
   buildInputs = [ zlib ];
diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix
index 1527f5d3ddad..e7f5eab8bfaf 100644
--- a/pkgs/applications/science/biology/strelka/default.nix
+++ b/pkgs/applications/science/biology/strelka/default.nix
@@ -2,16 +2,17 @@
 
 stdenv.mkDerivation rec {
   name = "strelka-${version}";
-  version = "2.9.5";
+  version = "2.9.10";
 
   src = fetchFromGitHub {
     owner = "Illumina";
     repo = "strelka";
     rev = "v${version}";
-    sha256 = "0x4a6nkx1jnyag9svghsdjz1fz6q7qx5pn77wphdfnk81f9yspf8";
+    sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf";
   };
 
-  buildInputs = [ cmake zlib python2 ];
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ zlib python2 ];
 
   preConfigure = ''
     sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py
diff --git a/pkgs/applications/science/biology/sumatools/default.nix b/pkgs/applications/science/biology/sumatools/default.nix
index 6f7227d7a3e9..f9042f300113 100644
--- a/pkgs/applications/science/biology/sumatools/default.nix
+++ b/pkgs/applications/science/biology/sumatools/default.nix
@@ -23,6 +23,7 @@ in rec {
       sha256 = "0hwkrxzfz7m5wdjvmrhkjg8kis378iaqr5n4nhdhkwwhn8x1jn5a";
     };
     makeFlags = "PREFIX=$(out)";
+    inherit meta;
   };
 
   # Sumatra
@@ -42,6 +43,7 @@ in rec {
       "LIBSUMAPATH=-L${sumalibs}"
       "PREFIX=$(out)"
     ];
+    inherit meta;
   };
 
   # Sumaclust
@@ -61,5 +63,6 @@ in rec {
       "LIBSUMAPATH=-L${sumalibs}"
       "PREFIX=$(out)"
     ];
+    inherit meta;
   };
 }