Add 'nixpkgs/' from commit 'abf060725d7614bd3b9f96764262dfbc2f9c2199'

git-subtree-dir: nixpkgs
git-subtree-mainline: 4e31070265257dc67d120c27e0f75c2344fdfa9a
git-subtree-split: abf060725d7614bd3b9f96764262dfbc2f9c2199

8 files changed, 244 insertions, 0 deletions

diff --git a/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix
new file mode 100644
index 000000000000..f4353f51d66c
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/biology/EBTKS/default.nix
@@ -0,0 +1,26 @@
+{ stdenv, fetchFromGitHub, cmake, libminc }:
+
+stdenv.mkDerivation rec {
+  pname = "EBTKS";
+  name  = "${pname}-2017-09-23";
+
+  src = fetchFromGitHub {
+    owner  = "BIC-MNI";
+    repo   = pname;
+    rev    = "67e4e197d8a32d6462c9bdc7af44d64ebde4fb5c";
+    sha256 = "1a1qw6i47fs1izx60l1ysabpmyx9j5sjnbdv8b47wi2xcc9i3hpq";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ libminc ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/BIC-MNI/${pname}";
+    description = "Library for working with MINC files";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license   = licenses.free;
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix
new file mode 100644
index 000000000000..3c9b8f8257ce
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/biology/bicgl/default.nix
@@ -0,0 +1,28 @@
+{ stdenv, fetchFromGitHub, cmake, libminc, bicpl, freeglut, mesa_glu }:
+
+stdenv.mkDerivation rec {
+  pname = "bicgl";
+  name  = "${pname}-2017-09-10";
+
+  owner = "BIC-MNI";
+
+  src = fetchFromGitHub {
+    inherit owner;
+    repo   = pname;
+    rev    = "b7f7e52d1039d6202a93d9055f516186033656cc";
+    sha256 = "0lzirdi1mf4yl8srq7vjn746sbydz7h0wjh7wy8gycy6hq04qrg4";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ libminc bicpl freeglut mesa_glu ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" "-DBICPL_DIR=${bicpl}/lib" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/${owner}/${pname}";
+    description = "Brain Imaging Centre graphics library";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license   = licenses.free;
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix
new file mode 100644
index 000000000000..f763e8a4fcc0
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/biology/bicpl/default.nix
@@ -0,0 +1,32 @@
+{ stdenv, fetchFromGitHub, cmake, libminc, netpbm }:
+
+stdenv.mkDerivation rec {
+  pname = "bicpl";
+  name  = "${pname}-2017-09-10";
+
+  owner = "BIC-MNI";
+
+  # current master is significantly ahead of most recent release, so use Git version:
+  src = fetchFromGitHub {
+    inherit owner;
+    repo   = pname;
+    rev    = "612a63e740fadb162fcf27ee00da6a18dec4d5a9";
+    sha256 = "1vv9gi184bkvp3f99v9xmmw1ly63ip5b09y7zdjn39g7kmwzrga7";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ libminc netpbm ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" "-DBUILD_TESTING=FALSE" ];
+
+  doCheck = false;
+  # internal_volume_io.h: No such file or directory
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/${owner}/${pname}";
+    description = "Brain Imaging Centre programming library";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license   = licenses.free;
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix
new file mode 100644
index 000000000000..5f4cbbaa5670
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/biology/elastix/default.nix
@@ -0,0 +1,23 @@
+{ stdenv, fetchurl, cmake, itk, python }:
+
+stdenv.mkDerivation rec {
+  pname    = "elastix";
+  pversion = "4.9.0";
+  name  = "${pname}-${pversion}";
+
+  src = fetchurl {
+    url    = "https://github.com/SuperElastix/${pname}/archive/${pversion}.tar.gz";
+    sha256 = "02pbln36nq98xxfyqwlxg7b6gmigdq4fgfqr9mym1qn58aj04shg";
+  };
+
+  nativeBuildInputs = [ cmake python ];
+  buildInputs = [ itk ];
+
+  meta = with stdenv.lib; {
+    homepage = http://elastix.isi.uu.nl/;
+    description = "Image registration toolkit based on ITK";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.linux;
+    license = licenses.asl20;
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix
new file mode 100644
index 000000000000..2ee9144b316d
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/biology/htslib/default.nix
@@ -0,0 +1,37 @@
+{ stdenv, fetchurl, zlib, bzip2, lzma, curl, perl }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "htslib";
+  version = "1.9";
+
+  src = fetchurl {
+    url = "https://github.com/samtools/htslib/releases/download/${version}/${name}.tar.bz2";
+    sha256 = "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0";
+  };
+
+  # perl is only used during the check phase.
+  nativeBuildInputs = [ perl ];
+
+  buildInputs = [ zlib bzip2 lzma curl ];
+
+  configureFlags = [ "--enable-libcurl" ]; # optional but strongly recommended
+
+  installFlags = "prefix=$(out)";
+
+  preCheck = ''
+    patchShebangs test/
+  '';
+
+  enableParallelBuilding = true;
+
+  doCheck = true;
+
+  meta = with stdenv.lib; {
+    description = "A C library for reading/writing high-throughput sequencing data";
+    license = licenses.mit;
+    homepage = http://www.htslib.org/;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.mimadrid ];
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix
new file mode 100644
index 000000000000..ce2050e82e6d
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/biology/mirtk/default.nix
@@ -0,0 +1,42 @@
+{ stdenv, lib, gtest, fetchFromGitHub, cmake, boost, eigen, python, vtk, zlib }:
+
+stdenv.mkDerivation rec {
+  version = "2.0.0";
+  name = "mirtk-${version}";
+
+  src = fetchFromGitHub {
+    owner = "BioMedIA";
+    repo = "MIRTK";
+    rev = "v${version}";
+    sha256 = "0i2v97m66ir5myvi5b123r7zcagwy551b73s984gk7lksl5yiqxk";
+    fetchSubmodules = true;
+  };
+
+  cmakeFlags = "-DWITH_VTK=ON -DBUILD_ALL_MODULES=ON -DBUILD_TESTING=ON";
+
+  doCheck = true;
+
+  checkPhase = ''
+    ctest -E '(Polynomial|ConvolutionFunction|Downsampling|EdgeTable|InterpolateExtrapolateImage)'
+  '';
+  # testPolynomial - segfaults for some reason
+  # testConvolutionFunction, testDownsampling - main not called correctly
+  # testEdgeTable, testInterpolateExtrapolateImageFunction - setup fails
+
+  postInstall = ''
+    install -Dm644 -t "$out/share/bash-completion/completions/mirtk" share/completion/bash/mirtk
+  '';
+
+  enableParallelBuilding = true;
+
+  nativeBuildInputs = [ cmake gtest ];
+  buildInputs = [ boost eigen python vtk zlib ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/BioMedIA/MIRTK";
+    description = "Medical image registration library and tools";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.linux;
+    license = licenses.asl20;
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix
new file mode 100644
index 000000000000..51eed36312dd
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/biology/nifticlib/default.nix
@@ -0,0 +1,25 @@
+{ stdenv, fetchurl, cmake, zlib }:
+
+stdenv.mkDerivation rec {
+  pname    = "nifticlib";
+  pversion = "2.0.0";
+  name  = "${pname}-${pversion}";
+
+  src = fetchurl {
+    url    = "mirror://sourceforge/project/niftilib/${pname}/${pname}_2_0_0/${name}.tar.gz";
+    sha256 = "123z9bwzgin5y8gi5ni8j217k7n683whjsvg0lrpii9flgk8isd3";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ zlib ];
+
+  doCheck = false; # fails 7 out of 293 tests
+
+  meta = with stdenv.lib; {
+    homepage = https://sourceforge.net/projects/niftilib;
+    description = "Medical imaging format C API";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.linux;
+    license = licenses.publicDomain;
+  };
+}
diff --git a/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix b/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix
new file mode 100644
index 000000000000..8755b7fd2eba
--- /dev/null
+++ b/nixpkgs/pkgs/development/libraries/science/biology/oobicpl/default.nix
@@ -0,0 +1,31 @@
+{ stdenv, fetchFromGitHub, cmake, libminc, bicpl, arguments, pcre-cpp }:
+
+stdenv.mkDerivation rec {
+  pname = "oobicpl";
+  name  = "${pname}-2016-03-02";
+
+  owner = "BIC-MNI";
+
+  src = fetchFromGitHub {
+    inherit owner;
+    repo   = pname;
+    rev    = "bc062a65dead2e58461f5afb37abedfa6173f10c";
+    sha256 = "05l4ml9djw17bgdnrldhcxydrzkr2f2scqlyak52ph5azj5n4zsx";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ libminc bicpl arguments pcre-cpp ];
+
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib"
+                 "-DBICPL_DIR=${bicpl}/lib"
+                 "-DARGUMENTS_DIR=${arguments}/lib"
+                 "-DOOBICPL_BUILD_SHARED_LIBS=TRUE" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/${owner}/${pname}";
+    description = "Brain Imaging Centre object-oriented programming library (and tools)";
+    maintainers = with maintainers; [ bcdarwin ];
+    platforms = platforms.unix;
+    license   = licenses.free;
+  };
+}