Merge commit '683c68232e91f76386db979c461d8fbe2a018782'

7 files changed, 96 insertions, 23 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix
index 978615fa4592..7502a4ffd2ab 100644
--- a/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix
@@ -1,18 +1,18 @@
-{ stdenv, fetchFromGitHub, cmake, pkgconfig, libminc, bicpl, itk, fftwFloat, gsl }:
+{ stdenv, fetchFromGitHub, cmake, pkgconfig, libminc, bicpl, itk4, fftwFloat, gsl }:
 
 stdenv.mkDerivation rec {
   pname = "EZminc";
-  name  = "${pname}-unstable-2019-07-25";
+  name  = "${pname}-unstable-2019-03-12";
 
   src = fetchFromGitHub {
     owner  = "BIC-MNI";
     repo   = pname;
-    rev    = "9591edd5389a5bda2c1f606816c7cdb35c065adf";
-    sha256 = "02k87qbpx0f48l2lbcjmlqx82py684z3sfi29va5icfg3hjd6j7b";
+    rev    = "5e3333ee356f914d34d66d33ea8df809c7f7fa51";
+    sha256 = "0wy8cppf5xpgfqvgb3mqs1cjh81n6qzkk6zxv29wvng8nar9wsy4";
   };
 
   nativeBuildInputs = [ cmake pkgconfig ];
-  buildInputs = [ itk libminc bicpl fftwFloat gsl ];
+  buildInputs = [ itk4 libminc bicpl fftwFloat gsl ];
 
   cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/"
                  "-DEZMINC_BUILD_TOOLS=TRUE"
diff --git a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
index 8ea3588fa8ca..59b173ac98cd 100644
--- a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
@@ -6,14 +6,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "1.0.20190902";
+  version = "1.0.20200331";
   pname = "dcm2niix";
 
   src = fetchFromGitHub {
     owner = "rordenlab";
     repo = "dcm2niix";
     rev = "v${version}";
-    sha256 = "0h8jsadgv831lqb0jhnaxm7lldirmnp5agrhgg5bcxvn860fl15b";
+    sha256 = "1cncfwhyhmg18n970lkn6yvp0i74ajznsl8dqz00asqfzmg681n1";
   };
 
   enableParallelBuilding = true;
diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
index 569c63afa7a1..21af5b82207b 100644
--- a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
@@ -4,8 +4,8 @@ let
   hts-nim = fetchFromGitHub {
     owner = "brentp";
     repo = "hts-nim";
-    rev = "v0.2.14";
-    sha256 = "0d1z4b6mrppmz3hgkxd4wcy79w68icvhi7q7n3m2k17n8f3xbdx3";
+    rev = "v0.3.4";
+    sha256 = "0670phk1bq3l9j2zaa8i5wcpc5dyfrc0l2a6c21g0l2mmdczffa7";
   };
 
   docopt = fetchFromGitHub {
@@ -17,13 +17,13 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "mosdepth";
-  version = "0.2.6";
+  version = "0.2.9";
 
   src = fetchFromGitHub {
     owner = "brentp";
     repo = "mosdepth";
     rev = "v${version}";
-    sha256 = "0i9pl9lsli3y84ygxanrr525gfg8fs9h481944cbzsmqmbldwvgk";
+    sha256 = "01gm9gj2x2zs4yx6wk761fi1papi7qr3gp4ln1kkn8n2f9y9h849";
   };
 
   buildInputs = [ nim ];
diff --git a/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix b/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix
index 6959b2caab8a..528277e05e38 100644
--- a/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix
@@ -1,17 +1,17 @@
 { stdenv, lib, fetchFromGitHub, python, makeWrapper
-, eigen, fftw, libtiff, zlib, ants, bc
+, eigen, fftw, libtiff, libpng, zlib, ants, bc
 , qt5, libGL, libGLU, libX11, libXext
 , withGui ? true }:
 
 stdenv.mkDerivation rec {
   pname = "mrtrix";
-  version = "3.0_RC3_latest";
+  version = "3.0.0";
 
   src = fetchFromGitHub {
     owner  = "MRtrix3";
     repo   = "mrtrix3";
     rev    = version;
-    sha256 = "184nv524p8j94qicjy9l288bqcgl2yxqqs55a7042i0gfsnwp51c";
+    sha256 = "1vvmmbw3m0bdfwp4szr62ygzsvkj0ss91cx5zlkspsr1rff05f9b";
     fetchSubmodules = true;
   };
 
@@ -22,7 +22,9 @@ stdenv.mkDerivation rec {
     python
     fftw
     libtiff
-    zlib ] ++ lib.optionals withGui [
+    libpng
+    zlib
+  ] ++ lib.optionals withGui [
     libGL
     libGLU
     libX11
@@ -34,9 +36,14 @@ stdenv.mkDerivation rec {
   installCheckInputs = [ bc ];
 
   postPatch = ''
-    patchShebangs ./build ./configure ./run_tests ./bin/population_template
+    patchShebangs ./build ./configure ./run_tests ./bin/*
+
+    # patching interpreters before fixup is needed for tests:
+    patchShebangs ./bin/*
+    patchShebangs testing/binaries/data/vectorstats/*py
+
     substituteInPlace ./run_tests  \
-      --replace 'git submodule update --init >> $LOGFILE 2>&1' ""
+      --replace 'git submodule update --init $datadir >> $LOGFILE 2>&1' ""
   '';
 
   configurePhase = ''
@@ -50,7 +57,13 @@ stdenv.mkDerivation rec {
     (cd testing && ../build)
   '';
 
-  installCheckPhase = "./run_tests";
+  installCheckPhase = ''
+    ./run_tests units
+    ./run_tests binaries
+
+    # can also `./run_tests scripts`, but this fails due to lack of FSL package
+    # (and there's no convenient way to disable individual tests)
+  '';
   doInstallCheck = true;
 
   installPhase = ''
@@ -63,7 +76,9 @@ stdenv.mkDerivation rec {
 
   postInstall = ''
     for prog in $out/bin/*; do
-      wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]}
+      if [[ -x "$prog" ]]; then
+        wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]}
+      fi
     done
   '';
 
diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
index 246c98768101..5073d0f0f324 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 = "2.22.2";
+  version = "2.22.4";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "11mzz483f89pb2s8jmwhl12d0m6k41kmi4xh0i6hq69rxrqi8l4s";
+    sha256 = "0gzna5df8nk42l7mc0qbp9h73gwr1030jnw10fawjp6ql6213kdd";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/nixpkgs/pkgs/applications/science/biology/quast/default.nix b/nixpkgs/pkgs/applications/science/biology/quast/default.nix
new file mode 100644
index 000000000000..e3c3ea23c2c0
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/quast/default.nix
@@ -0,0 +1,58 @@
+{ stdenv, fetchurl, python3Packages, zlib, bash, coreutils }:
+
+let
+  pythonPackages = python3Packages;
+  inherit (pythonPackages) python;
+in
+
+pythonPackages.buildPythonApplication rec {
+  pname = "quast";
+  version = "5.0.2";
+
+  src = fetchurl {
+    url = "https://github.com/ablab/quast/releases/download/${pname}_${version}/${pname}-${version}.tar.gz";
+    sha256 = "13ml8qywbb4cc7wf2x7z5mz1rjqg51ab8wkizwcg4f6c40zgif6d";
+  };
+
+  pythonPath = with pythonPackages; [ simplejson joblib setuptools matplotlib ];
+
+  nativeBuildInputs = [ coreutils ];
+
+  buildInputs = [ zlib ] ++ pythonPath;
+
+  dontConfigure = true;
+
+  dontBuild = true;
+
+  installPhase = ''
+    substituteInPlace quast_libs/bedtools/Makefile \
+      --replace "/bin/bash" "${bash}/bin/bash"
+    mkdir -p "$out/${python.sitePackages}"
+    export PYTHONPATH="$out/${python.sitePackages}:$PYTHONPATH"
+    ${python.interpreter} setup.py install \
+      --install-lib=$out/${python.sitePackages} \
+      --prefix="$out"
+  '';
+
+   postFixup = ''
+   for file in $(find $out -type f -type f -perm /0111); do
+       old_rpath=$(patchelf --print-rpath $file) && \
+       patchelf --set-rpath $old_rpath:${stdenv.cc.cc.lib}/lib $file || true
+   done
+   # Link to the master program
+   ln -s $out/bin/quast.py $out/bin/quast
+  '';
+
+  dontPatchELF = true;
+
+  # Tests need to download data files, so manual run after packaging is needed
+  doCheck = false;
+
+  meta = with stdenv.lib ; {
+    description = "Evaluates genome assemblies by computing various metrics";
+    homepage = "https://github.com/ablab/quast";
+    license = licenses.gpl2;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.all;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
index 93a02a46bd88..12c865162425 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 = "2.52";
+  version = "2.53";
   src = fetchurl {
     url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz";
-    sha256 = "0gq3kbj910jsq591wylzjmd23srjlsssmrckmf46m4ysjqdqd8vm";
+    sha256 = "1zchds205nwdqch1246953dr8c0019yas178qbq3jypbxvmgq7pf";
   };
 
   buildInputs = [ zlib ];