Merge commit 'a2e06fc3423c4be53181b15c28dfbe0bcf67dd73'

11 files changed, 135 insertions, 27 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/delly/default.nix b/nixpkgs/pkgs/applications/science/biology/delly/default.nix
index bfdf5a1bb17e..a6c45f8aa44e 100644
--- a/nixpkgs/pkgs/applications/science/biology/delly/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/delly/default.nix
@@ -1,16 +1,25 @@
-{ stdenv, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }:
+{ stdenv, fetchpatch, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }:
 
-stdenv.mkDerivation rec {
+let
+  htslibPatch = fetchpatch {
+    url = "https://github.com/dellytools/delly/commit/0e5c710b0c5ea790bb39699d4cbd49cf4fb86f14.diff";
+    sha256 = "09bz1qqvzhdzm99hf9zgrv80kq9jlr1m2mdvx96p2hk5lpnbdl7y";
+    excludes = [ "src/htslib" ];
+  };
+
+in stdenv.mkDerivation rec {
   pname = "delly";
-  version = "0.8.1";
+  version = "0.8.2";
 
   src = fetchFromGitHub {
       owner = "dellytools";
       repo = pname;
       rev = "v${version}";
-      sha256 = "18gm86j1g1k4z1cjv2m5v9rsl1xqs2w3dhwcsnzx2mhkrvmlc4i1";
+      sha256 = "14bkmixz7737xj192ww96s3a20zc7xs7r04db8avw3ggi3i1s1cs";
   };
 
+  patches = [ htslibPatch ];
+
   buildInputs = [ zlib htslib bzip2 lzma ncurses boost ];
 
   EBROOTHTSLIB = htslib;
diff --git a/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix b/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix
index 1a6555e0d634..5a1bb187886b 100644
--- a/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix
@@ -2,19 +2,21 @@
 
 stdenv.mkDerivation rec {
   pname = "kallisto";
-  version = "0.46.1";
+  version = "0.46.2";
 
   src = fetchFromGitHub {
     repo = "kallisto";
     owner = "pachterlab";
     rev = "v${version}";
-    sha256 = "09ldgy70wziw51ma4a3b7vyrphzf2v1cnq1j5r1wwgfmx8fgbh2z";
+    sha256 = "0m0r2820ca3rch99md1zzbgkilmlfkhdkpys2lfnb87qxmf1jnmb";
   };
 
   nativeBuildInputs = [ autoconf cmake ];
 
   buildInputs = [ hdf5 zlib ];
 
+  cmakeFlags = [ "-DUSE_HDF5=ON" ];
+
   # Parallel build fails in some cases: https://github.com/pachterlab/kallisto/issues/160
   enableParallelBuilding = false;
 
diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix
index c9e546dc2ce7..b47ce6ac3a94 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 = "1045";
+  version = "1047";
 
   src = fetchurl {
     url = "http://last.cbrc.jp/last-${version}.zip";
-    sha256 = "0x2wrm52ca935n3yc486m8yy59ap34w1x9h3csjca3jab5agnjkc";
+    sha256 = "06fj4qfw3dd35y3pky3dnr40v1alf43wjx373rbx1vr3hbgzvgf8";
   };
 
   nativeBuildInputs = [ unzip ];
diff --git a/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix
index 033f78609e9a..4c8b768a56a9 100644
--- a/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix
@@ -1,21 +1,28 @@
-{ stdenv, fetchFromGitHub, cmake, makeWrapper, flex, bison, perlPackages, libminc, libjpeg, zlib }:
+{ stdenv, fetchFromGitHub, cmake, makeWrapper, flex, bison, perl, TextFormat,
+  libminc, libjpeg, nifticlib, zlib }:
 
 stdenv.mkDerivation rec {
-  pname = "minc-tools";
-  name  = "${pname}-2017-09-11";
+  pname   = "minc-tools";
+  version = "unstable-2019-12-04";
 
   src = fetchFromGitHub {
     owner  = "BIC-MNI";
     repo   = pname;
-    rev    = "5b7c40425cd4f67a018055cb85c0157ee50a3056";
-    sha256 = "0zkcs05svp1gj5h0cdgc0k20c7lrk8m7wg3ks3xc5mkaiannj8g7";
+    rev    = "d4dddfdb4e4fa0cea389b8fdce51cfc076565d94";
+    sha256 = "1wwdss59qq4hz1jp35qylfswzzv0d37if23al0srnxkkgc5f8zng";
   };
 
+  patches = [ ./fix-netcdf-header.patch ];
+
   nativeBuildInputs = [ cmake flex bison makeWrapper ];
   buildInputs = [ libminc libjpeg zlib ];
-  propagatedBuildInputs = with perlPackages; [ perl TextFormat ];
+  propagatedBuildInputs = [ perl TextFormat ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ];
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/"
+                 "-DZNZ_INCLUDE_DIR=${nifticlib}/include/"
+                 "-DZNZ_LIBRARY=${nifticlib}/lib/libznz.a"
+                 "-DNIFTI_INCLUDE_DIR=${nifticlib}/include/nifti/"
+                 "-DNIFTI_LIBRARY=${nifticlib}/lib/libniftiio.a" ];
 
   postFixup = ''
     for prog in minccomplete minchistory mincpik; do
diff --git a/nixpkgs/pkgs/applications/science/biology/minc-tools/fix-netcdf-header.patch b/nixpkgs/pkgs/applications/science/biology/minc-tools/fix-netcdf-header.patch
new file mode 100644
index 000000000000..89c7564f8b62
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/minc-tools/fix-netcdf-header.patch
@@ -0,0 +1,12 @@
+diff --git a/progs/mincdump/mincdump.h b/progs/mincdump/mincdump.h
+index 14c95cd..117ab26 100644
+--- a/progs/mincdump/mincdump.h
++++ b/progs/mincdump/mincdump.h
+@@ -3,6 +3,7 @@
+  *   See netcdf/COPYRIGHT file for copying and redistribution conditions.
+  *   $Header: /private-cvsroot/minc/progs/mincdump/mincdump.h,v 1.1 2004-04-27 15:35:15 bert Exp $
+  *********************************************************************/
++#include <netcdf_meta.h>
+ 
+ 
+ /* error checking macro */
diff --git a/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix b/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix
new file mode 100644
index 000000000000..6959b2caab8a
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix
@@ -0,0 +1,77 @@
+{ stdenv, lib, fetchFromGitHub, python, makeWrapper
+, eigen, fftw, libtiff, zlib, ants, bc
+, qt5, libGL, libGLU, libX11, libXext
+, withGui ? true }:
+
+stdenv.mkDerivation rec {
+  pname = "mrtrix";
+  version = "3.0_RC3_latest";
+
+  src = fetchFromGitHub {
+    owner  = "MRtrix3";
+    repo   = "mrtrix3";
+    rev    = version;
+    sha256 = "184nv524p8j94qicjy9l288bqcgl2yxqqs55a7042i0gfsnwp51c";
+    fetchSubmodules = true;
+  };
+
+  nativeBuildInputs = [ eigen makeWrapper ] ++ lib.optional withGui qt5.wrapQtAppsHook;
+
+  buildInputs = [
+    ants
+    python
+    fftw
+    libtiff
+    zlib ] ++ lib.optionals withGui [
+    libGL
+    libGLU
+    libX11
+    libXext
+    qt5.qtbase
+    qt5.qtsvg
+  ];
+
+  installCheckInputs = [ bc ];
+
+  postPatch = ''
+    patchShebangs ./build ./configure ./run_tests ./bin/population_template
+    substituteInPlace ./run_tests  \
+      --replace 'git submodule update --init >> $LOGFILE 2>&1' ""
+  '';
+
+  configurePhase = ''
+    export EIGEN_CFLAGS="-isystem ${eigen}/include/eigen3"
+    unset LD  # similar to https://github.com/MRtrix3/mrtrix3/issues/1519
+    ./configure ${lib.optionalString (!withGui) "-nogui"};
+  '';
+
+  buildPhase = ''
+    ./build
+    (cd testing && ../build)
+  '';
+
+  installCheckPhase = "./run_tests";
+  doInstallCheck = true;
+
+  installPhase = ''
+    runHook preInstall
+    mkdir -p $out
+    cp -ar lib $out/lib
+    cp -ar bin $out/bin
+    runHook postInstall
+  '';
+
+  postInstall = ''
+    for prog in $out/bin/*; do
+      wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]}
+    done
+  '';
+
+  meta = with lib; {
+    homepage = "https://github.com/MRtrix3/mrtrix3";
+    description = "Suite of tools for diffusion imaging";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.linux;
+    license   = licenses.mpl20;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
index 44247f294aa6..93f66810549b 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 = "2.21.6";
+  version = "2.22.0";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "1vpyzhrs3bbviwk2n7k5296rnsw7g9ksvjsibl0gm7dawip9jb5s";
+    sha256 = "1qgg8r81xn2z965v78kfj05vycrd2cz48gxk5csr6kvwk3ba286c";
   };
 
   nativeBuildInputs = [ makeWrapper ];
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
   meta = with stdenv.lib; {
     description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF";
     license = licenses.mit;
-    homepage = https://broadinstitute.github.io/picard/;
+    homepage = "https://broadinstitute.github.io/picard/";
     maintainers = with maintainers; [ jbedo ];
     platforms = platforms.all;
   };
diff --git a/nixpkgs/pkgs/applications/science/biology/poretools/default.nix b/nixpkgs/pkgs/applications/science/biology/poretools/default.nix
index 8a19ae135e87..4660a776ab21 100755
--- a/nixpkgs/pkgs/applications/science/biology/poretools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/poretools/default.nix
@@ -16,7 +16,7 @@ pythonPackages.buildPythonPackage rec {
   meta = {
     description = "a toolkit for working with nanopore sequencing data from Oxford Nanopore";
     license = stdenv.lib.licenses.mit;
-    homepage = http://poretools.readthedocs.io/en/latest/;
+    homepage = https://poretools.readthedocs.io/en/latest/;
     maintainers = [stdenv.lib.maintainers.rybern];
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/biology/seaview/default.nix b/nixpkgs/pkgs/applications/science/biology/seaview/default.nix
index 69dece88c276..fea8da41d70a 100644
--- a/nixpkgs/pkgs/applications/science/biology/seaview/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/seaview/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchurl, coreutils, fltk, libjpeg }:
 
 stdenv.mkDerivation rec {
-  version = "4.7";
+  version = "5.0";
   pname = "seaview";
 
   src = fetchurl {
     url = "ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_${version}.tar.gz";
-    sha256 = "0fhyq7dcn0izhwcfin9ajsr7kmmsqm9f1np1rmhzg4digfwqb29n";
+    sha256 = "0gzjqf5mm91pa1drwxvz229bv6l995npdggngszh6z6j4pfh8j7c";
   };
 
   buildInputs = [ fltk libjpeg ];
diff --git a/nixpkgs/pkgs/applications/science/biology/spades/default.nix b/nixpkgs/pkgs/applications/science/biology/spades/default.nix
index a195f79010a7..08a6a0d25095 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 = "3.13.1";
+  version = "3.14.0";
 
   src = fetchurl {
     url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz";
-    sha256 = "0giayz197lmq2108filkn9izma3i803sb3iskv9hs5snzdr9p8ld";
+    sha256 = "1ffxswd2ngkpy1d6l3lb6a9cmyy1fglbdsws00b3m1k22zaqv60q";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/nixpkgs/pkgs/applications/science/biology/truvari/default.nix b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix
index bee43da6719d..e64c9d3493e9 100644
--- a/nixpkgs/pkgs/applications/science/biology/truvari/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix
@@ -5,13 +5,13 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "truvari";
-  version = "1.3.2";
+  version = "1.3.4";
 
   src = fetchFromGitHub {
     owner = "spiralgenetics";
     repo = "truvari";
     rev = "v${version}";
-    sha256 = "0wmjz8nzibvj0ixky1m0qi7iyd204prk7glbvig1cvaab33k19f1";
+    sha256 = "1bph7v48s7pyfagz8a2fzl5fycjliqzn5lcbv3m2bp2ih1f1gd1v";
   };
 
   propagatedBuildInputs = with python3Packages; [
@@ -25,8 +25,9 @@ python3Packages.buildPythonApplication rec {
 
   prePatch = ''
     substituteInPlace ./setup.py \
-      --replace '"progressbar2==3.41.0",' "" \
-      --replace '"pysam==0.15.2",' ""
+      --replace '"progressbar2==3.41.0",' '"progressbar2==3.47.0",' \
+      --replace '"pysam==0.15.2",' '"pysam==0.15.4",' \
+      --replace '"pyfaidx==0.5.5.2",' '"pyfaidx==0.5.8",'
   '';
 
   meta = with lib; {