diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index b90a0eea177..e4b10cdf536 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -490,6 +490,21 @@ version.joined       123
    Python properties don't need parentheses. ``version.dashed`` is correct.
    ``version.dashed()`` is incorrect.
 
+In addition, these version properties can be combined with ``up_to()``.
+For example:
+
+.. code-block:: python
+
+   >>> version = Version('1.2.3')
+   >>> version.up_to(2).dashed
+   Version('1-2')
+   >>> version.underscored.up_to(2)
+   Version('1_2')
+
+
+As you can see, order is not important. Just keep in mind that ``up_to()`` and
+the other version properties return ``Version`` objects, not strings.
+
 If a URL cannot be derived systematically, or there is a special URL for one
 of its versions, you can add an explicit URL for a particular version:
 
diff --git a/lib/spack/spack/build_systems/autotools.py b/lib/spack/spack/build_systems/autotools.py
index 1ef38ddc2db..230e12e1f85 100644
--- a/lib/spack/spack/build_systems/autotools.py
+++ b/lib/spack/spack/build_systems/autotools.py
@@ -98,7 +98,9 @@ class AutotoolsPackage(PackageBase):
     @run_after('autoreconf')
     def _do_patch_config_guess(self):
         """Some packages ship with an older config.guess and need to have
-        this updated when installed on a newer architecture."""
+        this updated when installed on a newer architecture. In particular,
+        config.guess fails for PPC64LE for version prior to a 2013-06-10
+        build date (automake 1.13.4)."""
 
         if not self.patch_config_guess or not self.spec.satisfies(
                 'arch=linux-rhel7-ppc64le'
@@ -190,20 +192,6 @@ def default_flag_handler(self, spack_env, flag_val):
                       ' '.join(flag_val[1]))
         return []
 
-    def patch(self):
-        """Patches config.guess if
-        :py:attr:``~.AutotoolsPackage.patch_config_guess`` is True
-
-        :raise RuntimeError: if something goes wrong when patching
-            ``config.guess``
-        """
-
-        if self.patch_config_guess and self.spec.satisfies(
-                'arch=linux-rhel7-ppc64le'
-        ):
-            if not self._do_patch_config_guess():
-                raise RuntimeError('Failed to find suitable config.guess')
-
     @run_before('autoreconf')
     def delete_configure_to_force_update(self):
         if self.force_autoreconf:
diff --git a/lib/spack/spack/build_systems/cmake.py b/lib/spack/spack/build_systems/cmake.py
index b339858348b..db3240e8a52 100644
--- a/lib/spack/spack/build_systems/cmake.py
+++ b/lib/spack/spack/build_systems/cmake.py
@@ -29,7 +29,7 @@
 
 import spack.build_environment
 from llnl.util.filesystem import working_dir, join_path
-from spack.directives import depends_on
+from spack.directives import depends_on, variant
 from spack.package import PackageBase, run_after
 
 
@@ -49,11 +49,6 @@ class CMakePackage(PackageBase):
         +-----------------------------------------------+--------------------+
         | **Method**                                    | **Purpose**        |
         +===============================================+====================+
-        | :py:meth:`~.CMakePackage.build_type`          | Specify the value  |
-        |                                               | for the            |
-        |                                               | CMAKE_BUILD_TYPE   |
-        |                                               | variable           |
-        +-----------------------------------------------+--------------------+
         | :py:meth:`~.CMakePackage.root_cmakelists_dir` | Location of the    |
         |                                               | root CMakeLists.txt|
         +-----------------------------------------------+--------------------+
@@ -74,15 +69,13 @@ class CMakePackage(PackageBase):
 
     build_time_test_callbacks = ['check']
 
+    # https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html
+    variant('build_type', default='RelWithDebInfo',
+            description='The build type to build',
+            values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel'))
+
     depends_on('cmake', type='build')
 
-    def build_type(self):
-        """Returns the correct value for the ``CMAKE_BUILD_TYPE`` variable
-
-        :return: value for ``CMAKE_BUILD_TYPE``
-        """
-        return 'RelWithDebInfo'
-
     @property
     def root_cmakelists_dir(self):
         """The relative path to the directory containing CMakeLists.txt
@@ -108,8 +101,8 @@ def std_cmake_args(self):
     def _std_args(pkg):
         """Computes the standard cmake arguments for a generic package"""
         try:
-            build_type = pkg.build_type()
-        except AttributeError:
+            build_type = pkg.spec.variants['build_type'].value
+        except KeyError:
             build_type = 'RelWithDebInfo'
 
         args = ['-DCMAKE_INSTALL_PREFIX:PATH={0}'.format(pkg.prefix),
diff --git a/lib/spack/spack/test/url_parse.py b/lib/spack/spack/test/url_parse.py
index 6789bc0aa3a..41a2fda649d 100644
--- a/lib/spack/spack/test/url_parse.py
+++ b/lib/spack/spack/test/url_parse.py
@@ -107,7 +107,9 @@
     # Combinations of multiple patterns - public
     ('dakota-6.3-public.src', 'dakota-6.3'),
     # Combinations of multiple patterns - universal
-    ('synergy-1.3.6p2-MacOSX-Universal', 'synergy-1.3.6p2')
+    ('synergy-1.3.6p2-MacOSX-Universal', 'synergy-1.3.6p2'),
+    # Combinations of multiple patterns - dynamic
+    ('snptest_v2.5.2_linux_x86_64_dynamic', 'snptest_v2.5.2'),
 ])
 def test_url_strip_version_suffixes(url, expected):
     stripped = strip_version_suffixes(url)
diff --git a/lib/spack/spack/test/versions.py b/lib/spack/spack/test/versions.py
index 3b04e1d4aa4..72292e4dcd0 100644
--- a/lib/spack/spack/test/versions.py
+++ b/lib/spack/spack/test/versions.py
@@ -204,6 +204,8 @@ def test_underscores():
     assert_ver_eq('2_0', '2_0')
     assert_ver_eq('2.0', '2_0')
     assert_ver_eq('2_0', '2.0')
+    assert_ver_eq('2-0', '2_0')
+    assert_ver_eq('2_0', '2-0')
 
 
 def test_rpm_oddities():
@@ -426,20 +428,56 @@ def test_satisfaction_with_lists():
 
 
 def test_formatted_strings():
-    versions = '1.2.3', '1_2_3', '1-2-3'
+    versions = (
+        '1.2.3b', '1_2_3b', '1-2-3b',
+        '1.2-3b', '1.2_3b', '1-2.3b',
+        '1-2_3b', '1_2.3b', '1_2-3b'
+    )
     for item in versions:
         v = Version(item)
-        assert v.dotted == '1.2.3'
-        assert v.dashed == '1-2-3'
-        assert v.underscored == '1_2_3'
-        assert v.joined == '123'
+        assert v.dotted.string == '1.2.3b'
+        assert v.dashed.string == '1-2-3b'
+        assert v.underscored.string == '1_2_3b'
+        assert v.joined.string == '123b'
+
+        assert v.dotted.dashed.string == '1-2-3b'
+        assert v.dotted.underscored.string == '1_2_3b'
+        assert v.dotted.dotted.string == '1.2.3b'
+        assert v.dotted.joined.string == '123b'
+
+
+def test_up_to():
+    v = Version('1.23-4_5b')
+
+    assert v.up_to(1).string == '1'
+    assert v.up_to(2).string == '1.23'
+    assert v.up_to(3).string == '1.23-4'
+    assert v.up_to(4).string == '1.23-4_5'
+    assert v.up_to(5).string == '1.23-4_5b'
+
+    assert v.up_to(-1).string == '1.23-4_5'
+    assert v.up_to(-2).string == '1.23-4'
+    assert v.up_to(-3).string == '1.23'
+    assert v.up_to(-4).string == '1'
+
+    assert v.up_to(2).dotted.string == '1.23'
+    assert v.up_to(2).dashed.string == '1-23'
+    assert v.up_to(2).underscored.string == '1_23'
+    assert v.up_to(2).joined.string == '123'
+
+    assert v.dotted.up_to(2).string == '1.23' == v.up_to(2).dotted.string
+    assert v.dashed.up_to(2).string == '1-23' == v.up_to(2).dashed.string
+    assert v.underscored.up_to(2).string == '1_23'
+    assert v.up_to(2).underscored.string == '1_23'
+
+    assert v.up_to(2).up_to(1).string == '1'
 
 
 def test_repr_and_str():
 
     def check_repr_and_str(vrs):
         a = Version(vrs)
-        assert repr(a) == 'Version(\'' + vrs + '\')'
+        assert repr(a) == "Version('" + vrs + "')"
         b = eval(repr(a))
         assert a == b
         assert str(a) == vrs
@@ -457,17 +495,17 @@ def test_get_item():
     b = a[0:2]
     assert isinstance(b, Version)
     assert b == Version('0.1')
-    assert repr(b) == 'Version(\'0.1\')'
+    assert repr(b) == "Version('0.1')"
     assert str(b) == '0.1'
     b = a[0:3]
     assert isinstance(b, Version)
     assert b == Version('0.1_2')
-    assert repr(b) == 'Version(\'0.1_2\')'
+    assert repr(b) == "Version('0.1_2')"
     assert str(b) == '0.1_2'
     b = a[1:]
     assert isinstance(b, Version)
     assert b == Version('1_2-3')
-    assert repr(b) == 'Version(\'1_2-3\')'
+    assert repr(b) == "Version('1_2-3')"
     assert str(b) == '1_2-3'
     # Raise TypeError on tuples
     with pytest.raises(TypeError):
diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py
index d29ce3d07f8..e3da753a76a 100644
--- a/lib/spack/spack/url.py
+++ b/lib/spack/spack/url.py
@@ -177,6 +177,7 @@ def strip_version_suffixes(path):
         '[Uu]niversal',
         'jar',
         'complete',
+        'dynamic',
         'oss',
         'gem',
         'tar',
diff --git a/lib/spack/spack/version.py b/lib/spack/spack/version.py
index 10fac49e9d5..0d8520a0e0a 100644
--- a/lib/spack/spack/version.py
+++ b/lib/spack/spack/version.py
@@ -130,30 +130,90 @@ def __init__(self, string):
         self.version = tuple(int_if_int(seg) for seg in segments)
 
         # Store the separators from the original version string as well.
-        # last element of separators is ''
-        self.separators = tuple(re.split(segment_regex, string)[1:-1])
+        self.separators = tuple(re.split(segment_regex, string)[1:])
 
     @property
     def dotted(self):
-        return '.'.join(str(x) for x in self.version)
+        """The dotted representation of the version.
+
+        Example:
+        >>> version = Version('1-2-3b')
+        >>> version.dotted
+        Version('1.2.3b')
+
+        Returns:
+            Version: The version with separator characters replaced by dots
+        """
+        return Version(self.string.replace('-', '.').replace('_', '.'))
 
     @property
     def underscored(self):
-        return '_'.join(str(x) for x in self.version)
+        """The underscored representation of the version.
+
+        Example:
+        >>> version = Version('1.2.3b')
+        >>> version.underscored
+        Version('1_2_3b')
+
+        Returns:
+            Version: The version with separator characters replaced by
+                underscores
+        """
+        return Version(self.string.replace('.', '_').replace('-', '_'))
 
     @property
     def dashed(self):
-        return '-'.join(str(x) for x in self.version)
+        """The dashed representation of the version.
+
+        Example:
+        >>> version = Version('1.2.3b')
+        >>> version.dashed
+        Version('1-2-3b')
+
+        Returns:
+            Version: The version with separator characters replaced by dashes
+        """
+        return Version(self.string.replace('.', '-').replace('_', '-'))
 
     @property
     def joined(self):
-        return ''.join(str(x) for x in self.version)
+        """The joined representation of the version.
+
+        Example:
+        >>> version = Version('1.2.3b')
+        >>> version.joined
+        Version('123b')
+
+        Returns:
+            Version: The version with separator characters removed
+        """
+        return Version(
+            self.string.replace('.', '').replace('-', '').replace('_', ''))
 
     def up_to(self, index):
-        """Return a version string up to the specified component, exclusive.
-           e.g., if this is 10.8.2, self.up_to(2) will return '10.8'.
+        """The version up to the specified component.
+
+        Examples:
+        >>> version = Version('1.23-4b')
+        >>> version.up_to(1)
+        Version('1')
+        >>> version.up_to(2)
+        Version('1.23')
+        >>> version.up_to(3)
+        Version('1.23-4')
+        >>> version.up_to(4)
+        Version('1.23-4b')
+        >>> version.up_to(-1)
+        Version('1.23-4')
+        >>> version.up_to(-2)
+        Version('1.23')
+        >>> version.up_to(-3)
+        Version('1')
+
+        Returns:
+            Version: The first index components of the version
         """
-        return '.'.join(str(x) for x in self[:index])
+        return self[:index]
 
     def lowest(self):
         return self
@@ -204,11 +264,9 @@ def __getitem__(self, idx):
             return self.version[idx]
 
         elif isinstance(idx, slice):
-            # Currently len(self.separators) == len(self.version) - 1
-            extendend_separators = self.separators + ('',)
             string_arg = []
 
-            pairs = zip(self.version[idx], extendend_separators[idx])
+            pairs = zip(self.version[idx], self.separators[idx])
             for token, sep in pairs:
                 string_arg.append(str(token))
                 string_arg.append(str(sep))
diff --git a/var/spack/repos/builtin/packages/alquimia/package.py b/var/spack/repos/builtin/packages/alquimia/package.py
index b8d3f608406..cadea3cb3ca 100644
--- a/var/spack/repos/builtin/packages/alquimia/package.py
+++ b/var/spack/repos/builtin/packages/alquimia/package.py
@@ -36,8 +36,6 @@ class Alquimia(CMakePackage):
 
     variant('shared', default=True,
             description='Enables the build of shared libraries')
-    variant('debug',  default=False,
-            description='Builds a debug version of the libraries')
 
     depends_on('mpi')
     depends_on('hdf5')
@@ -52,10 +50,6 @@ def cmake_args(self):
         options = ['-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
                    '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
                    '-DUSE_XSDK_DEFAULTS=YES',
-                   '-DCMAKE_BUILD_TYPE:STRING=%s' % (
-                       'DEBUG' if '+debug' in spec else 'RELEASE'),
-                   '-DXSDK_ENABLE_DEBUG:STRING=%s' % (
-                       'YES' if '+debug' in spec else 'NO'),
                    '-DBUILD_SHARED_LIBS:BOOL=%s' % (
                        'ON' if '+shared' in spec else 'OFF'),
                    '-DTPL_ENABLE_MPI:BOOL=ON',
diff --git a/var/spack/repos/builtin/packages/benchmark/package.py b/var/spack/repos/builtin/packages/benchmark/package.py
index eecb9341d98..4101b0e9e09 100644
--- a/var/spack/repos/builtin/packages/benchmark/package.py
+++ b/var/spack/repos/builtin/packages/benchmark/package.py
@@ -37,6 +37,11 @@ class Benchmark(CMakePackage):
     version('1.1.0', '66b2a23076cf70739525be0092fc3ae3')
     version('1.0.0', '1474ff826f8cd68067258db75a0835b8')
 
+    variant('build_type', default='RelWithDebInfo',
+            description='The build type to build',
+            values=('Debug', 'Release', 'RelWithDebInfo',
+                    'MinSizeRel', 'Coverage'))
+
     def patch(self):
         filter_file(
             r'add_cxx_compiler_flag..fstrict.aliasing.',
diff --git a/var/spack/repos/builtin/packages/bml/package.py b/var/spack/repos/builtin/packages/bml/package.py
index 87dc1c9e80e..68e62032e4c 100644
--- a/var/spack/repos/builtin/packages/bml/package.py
+++ b/var/spack/repos/builtin/packages/bml/package.py
@@ -30,20 +30,11 @@ class Bml(CMakePackage):
     formats (in dense and sparse) and their associated algorithms for basic
     matrix operations."""
 
-    homepage = "https://github.com/qmmd/bml"
-    url      = "https://github.com/qmmd/bml"
+    homepage = "https://github.com/lanl/bml"
+    url      = "https://github.com/lanl/bml"
 
-    version('develop', git='https://github.com/qmmd/bml', branch='master')
-    version('1.1.0', git='https://github.com/qmmd/bml', tag='v1.1.0')
-
-    variant('debug', default=False, description='Build debug version')
+    version('develop', git='https://github.com/lanl/bml', branch='master')
+    version('1.1.0', git='https://github.com/lanl/bml', tag='v1.1.0')
 
     depends_on("blas")
     depends_on("lapack")
-
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
diff --git a/var/spack/repos/builtin/packages/caffe/package.py b/var/spack/repos/builtin/packages/caffe/package.py
index 4e2ef26dbb4..021814c7fd6 100644
--- a/var/spack/repos/builtin/packages/caffe/package.py
+++ b/var/spack/repos/builtin/packages/caffe/package.py
@@ -39,7 +39,7 @@ class Caffe(CMakePackage):
     version('rc3', '84e39223115753b48312a8bf48c31f59')
     version('rc2', 'c331932e34b5e2f5022fcc34c419080f')
 
-    variant('gpu', default=False,
+    variant('cuda', default=False,
             description='Builds with support for GPUs via CUDA and cuDNN')
     variant('opencv', default=True,
             description='Build with OpenCV support')
@@ -54,7 +54,7 @@ class Caffe(CMakePackage):
 
     depends_on('boost')
     depends_on('boost +python', when='+python')
-    depends_on('cuda', when='+gpu')
+    depends_on('cuda', when='+cuda')
     depends_on('blas')
     depends_on('protobuf')
     depends_on('glog')
@@ -75,8 +75,8 @@ def cmake_args(self):
         spec = self.spec
         args = ['-DBLAS={0}'.format('open' if spec['blas'].name == 'openblas'
                 else spec['blas'].name),
-                '-DCPU_ONLY=%s' % ('~gpu' in spec),
-                '-DUSE_CUDNN=%s' % ('+gpu' in spec),
+                '-DCPU_ONLY=%s' % ('~cuda' in spec),
+                '-DUSE_CUDNN=%s' % ('+cuda' in spec),
                 '-DBUILD_python=%s' % ('+python' in spec),
                 '-DBUILD_python_layer=%s' % ('+python' in spec),
                 '-DBUILD_matlab=%s' % ('+matlab' in spec),
diff --git a/var/spack/repos/builtin/packages/callpath/package.py b/var/spack/repos/builtin/packages/callpath/package.py
index 9ded62e5c5d..813e491dfdd 100644
--- a/var/spack/repos/builtin/packages/callpath/package.py
+++ b/var/spack/repos/builtin/packages/callpath/package.py
@@ -46,7 +46,9 @@ def install(self, spec, prefix):
         # TODO: offer options for the walker used.
         cmake_args = std_cmake_args
         if spec.satisfies("^dyninst@9.3.0:"):
-            cmake_args.append("-DCMAKE_CXX_FLAGS='-std=c++11 -fpermissive'")
+            std_flag = self.compiler.cxx11_flag
+            cmake_args.append("-DCMAKE_CXX_FLAGS='{0} -fpermissive'".format(
+                std_flag))
         cmake('.', "-DCALLPATH_WALKER=dyninst", *cmake_args)
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
index 2c1c6636393..a13d79c9539 100644
--- a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
@@ -53,6 +53,9 @@ class CbtfArgonavis(CMakePackage):
     version('1.8', branch='master',
             git='https://github.com/OpenSpeedShop/cbtf-argonavis.git')
 
+    variant('build_type', default='None', values=('None'),
+            description='CMake build type')
+
     depends_on("cmake@3.0.2:", type='build')
     depends_on("boost@1.50.0:1.59.0")
     depends_on("papi")
@@ -65,9 +68,6 @@ class CbtfArgonavis(CMakePackage):
 
     build_directory = 'build_cbtf_argonavis'
 
-    def build_type(self):
-        return 'None'
-
     def cmake_args(self):
         spec = self.spec
         compile_flags = "-O2 -g"
diff --git a/var/spack/repos/builtin/packages/cbtf-krell/package.py b/var/spack/repos/builtin/packages/cbtf-krell/package.py
index a90ea74f9d0..40fc932e8f3 100644
--- a/var/spack/repos/builtin/packages/cbtf-krell/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-krell/package.py
@@ -68,6 +68,8 @@ class CbtfKrell(CMakePackage):
             description="Build mpi experiment collector for mpich2 MPI.")
     variant('mpich', default=False,
             description="Build mpi experiment collector for mpich MPI.")
+    variant('build_type', default='None', values=('None'),
+            description='CMake build type')
 
     # Dependencies for cbtf-krell
     depends_on("cmake@3.0.2:", type='build')
@@ -129,9 +131,6 @@ def set_mpi_cmakeOptions(self, spec, cmakeOptions):
 
         cmakeOptions.extend(MPIOptions)
 
-    def build_type(self):
-        return 'None'
-
     def cmake_args(self):
         spec = self.spec
 
diff --git a/var/spack/repos/builtin/packages/cbtf-lanl/package.py b/var/spack/repos/builtin/packages/cbtf-lanl/package.py
index 6ffca1f8b16..b56265154c3 100644
--- a/var/spack/repos/builtin/packages/cbtf-lanl/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-lanl/package.py
@@ -51,6 +51,9 @@ class CbtfLanl(CMakePackage):
     version('1.8', branch='master',
             git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl')
 
+    variant('build_type', default='None', values=('None'),
+            description='CMake build type')
+
     depends_on("cmake@3.0.2:", type='build')
     # Dependencies for cbtf-krell
     depends_on("mrnet@5.0.1:+lwthreads")
@@ -62,9 +65,6 @@ class CbtfLanl(CMakePackage):
 
     build_directory = 'build_cbtf_lanl'
 
-    def build_type(self):
-        return 'None'
-
     def cmake_args(self):
 
         spec = self.spec
diff --git a/var/spack/repos/builtin/packages/cbtf/package.py b/var/spack/repos/builtin/packages/cbtf/package.py
index 68e2b7d0a22..d972544f5ff 100644
--- a/var/spack/repos/builtin/packages/cbtf/package.py
+++ b/var/spack/repos/builtin/packages/cbtf/package.py
@@ -58,6 +58,8 @@ class Cbtf(CMakePackage):
 
     variant('runtime', default=False,
             description="build only the runtime libraries and collectors.")
+    variant('build_type', default='None', values=('None'),
+            description='CMake build type')
 
     depends_on("cmake@3.0.2:", type='build')
     depends_on("boost@1.50.0:1.59.0")
@@ -70,9 +72,6 @@ class Cbtf(CMakePackage):
 
     build_directory = 'build_cbtf'
 
-    def build_type(self):
-        return 'None'
-
     def cmake_args(self):
 
         spec = self.spec
diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py
index 898f7ff1b8c..938dcdfb8c4 100644
--- a/var/spack/repos/builtin/packages/cdo/package.py
+++ b/var/spack/repos/builtin/packages/cdo/package.py
@@ -34,6 +34,8 @@ class Cdo(Package):
     url      = "https://code.zmaw.de/attachments/download/12760/cdo-1.7.2.tar.gz"
     list_url = "https://code.zmaw.de/projects/cdo/files"
 
+    version('1.8.2', '6a2e2f99b7c67ee9a512c40a8d4a7121',
+            url='https://code.zmaw.de/attachments/download/14686/cdo-1.8.2.tar.gz')
     version('1.7.2', 'f08e4ce8739a4f2b63fc81a24db3ee31',
             url='https://code.zmaw.de/attachments/download/12760/cdo-1.7.2.tar.gz')
     version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2',
diff --git a/var/spack/repos/builtin/packages/clamr/package.py b/var/spack/repos/builtin/packages/clamr/package.py
index c45069d39f5..d1eee12d1c0 100644
--- a/var/spack/repos/builtin/packages/clamr/package.py
+++ b/var/spack/repos/builtin/packages/clamr/package.py
@@ -41,10 +41,6 @@ class Clamr(CMakePackage):
         'graphics', default='opengl',
         values=('opengl', 'mpe', 'none'),
         description='Build with specified graphics support')
-    variant(
-        'build', default='relwithdebinfo',
-        values=('debug', 'release', 'relwithdebinfo'),
-        description='Build type')
     variant(
         'precision', default='mixed',
         values=('single', 'mixed', 'full'),
@@ -53,15 +49,6 @@ class Clamr(CMakePackage):
     depends_on('mpi')
     depends_on('mpe', when='graphics=mpe')
 
-    def build_type(self):
-        spec = self.spec
-        if 'build=debug' in spec:
-            return 'Debug'
-        elif 'build=release' in spec:
-            return 'Release'
-        else:
-            return 'RelWithDebInfo'
-
     def cmake_args(self):
         spec = self.spec
         cmake_args = []
diff --git a/var/spack/repos/builtin/packages/cleaveland4/package.py b/var/spack/repos/builtin/packages/cleaveland4/package.py
new file mode 100644
index 00000000000..505f800ac76
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cleaveland4/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Cleaveland4(Package):
+    """CleaveLand4: Analysis of degradome data to find sliced miRNA and siRNA
+       targets"""
+
+    homepage = "https://github.com/MikeAxtell/CleaveLand4"
+    url      = "https://github.com/MikeAxtell/CleaveLand4/archive/v4.4.tar.gz"
+
+    version('4.4', 'cf62a1de715a612fc8bd5a62364e69db')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('perl-math-cdf', type=('build', 'run'))
+    depends_on('bowtie')
+    depends_on('viennarna')
+    depends_on('r', type=('build', 'run'))
+    depends_on('samtools')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('CleaveLand4.pl', prefix.bin)
+        with working_dir('GSTAr_v1-0'):
+            install('GSTAr.pl', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/clhep/package.py b/var/spack/repos/builtin/packages/clhep/package.py
index 7120fffac6c..2f4f5b1579c 100644
--- a/var/spack/repos/builtin/packages/clhep/package.py
+++ b/var/spack/repos/builtin/packages/clhep/package.py
@@ -50,7 +50,6 @@ class Clhep(CMakePackage):
     version('2.2.0.5', '1584e8ce6ebf395821aed377df315c7c')
     version('2.2.0.4', '71d2c7c2e39d86a0262e555148de01c1')
 
-    variant('debug', default=False, description="Switch to the debug version of CLHEP.")
     variant('cxx11', default=True, description="Compile using c++11 dialect.")
     variant('cxx14', default=False, description="Compile using c++14 dialect.")
 
@@ -65,14 +64,6 @@ def patch(self):
 
     root_cmakelists_dir = 'CLHEP'
 
-    def build_type(self):
-        spec = self.spec
-
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'MinSizeRel'
-
     def cmake_args(self):
         spec = self.spec
         cmake_args = []
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index ba1f8960108..aa6a2be0b48 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -71,6 +71,9 @@ class Dealii(CMakePackage):
             description='Compile with 64 bit indices support')
     variant('optflags', default=False,
             description='Compile using additional optimization flags')
+    variant('build_type', default='DebugRelease',
+            description='The build type to build',
+            values=('Debug', 'Release', 'DebugRelease'))
 
     # required dependencies, light version
     depends_on("blas")
@@ -136,10 +139,6 @@ class Dealii(CMakePackage):
               '+slepc', '+trilinos']:
         conflicts(p, when='~mpi')
 
-    def build_type(self):
-        # CMAKE_BUILD_TYPE should be DebugRelease | Debug | Release
-        return 'DebugRelease'
-
     def cmake_args(self):
         spec = self.spec
         options = []
diff --git a/var/spack/repos/builtin/packages/eccodes/package.py b/var/spack/repos/builtin/packages/eccodes/package.py
index 137f445c690..40539e19c92 100644
--- a/var/spack/repos/builtin/packages/eccodes/package.py
+++ b/var/spack/repos/builtin/packages/eccodes/package.py
@@ -50,6 +50,9 @@ class Eccodes(CMakePackage):
             description="Enable OpenMP threads")
     variant('memfs', default=False,
             description="Memory based access to definitions/samples")
+    variant('build_type', default='RelWithDebInfo',
+            description='The build type to build',
+            values=('Debug', 'Release', 'RelWithDebInfo', 'Production'))
 
     depends_on('netcdf', when='+netcdf')
     depends_on('openjpeg', when='+jpeg')
diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py
index 0aefe416e36..569af17c61d 100644
--- a/var/spack/repos/builtin/packages/eigen/package.py
+++ b/var/spack/repos/builtin/packages/eigen/package.py
@@ -40,9 +40,6 @@ class Eigen(CMakePackage):
     version('3.2.8', '64f4aef8012a424c7e079eaf0be71793ab9bc6e0')
     version('3.2.7', 'cc1bacbad97558b97da6b77c9644f184')
 
-    variant('debug', default=False,
-            description='Builds the library in debug mode')
-
     variant('metis', default=True, description='Enables metis backend')
     variant('scotch', default=True, description='Enables scotch backend')
     variant('fftw', default=True, description='Enables FFTW backend')
@@ -50,6 +47,9 @@ class Eigen(CMakePackage):
             description='Enables SuiteSparse support')
     variant('mpfr', default=True,
             description='Enables support for multi-precisions FP via mpfr')
+    variant('build_type', default='RelWithDebInfo',
+            description='The build type to build',
+            values=('Debug', 'Release', 'RelWithDebInfo'))
 
     # TODO : dependency on googlehash, superlu, adolc missing
     depends_on('metis@5:', when='+metis')
@@ -58,9 +58,3 @@ class Eigen(CMakePackage):
     depends_on('suite-sparse', when='+suitesparse')
     depends_on('mpfr@2.3.0:', when='+mpfr')
     depends_on('gmp', when='+mpfr')
-
-    def build_type(self):
-        if '+debug' in self.spec:
-            return 'Debug'
-        else:
-            return 'Release'
diff --git a/var/spack/repos/builtin/packages/elemental/package.py b/var/spack/repos/builtin/packages/elemental/package.py
index d86ee985f76..e118bcbd447 100644
--- a/var/spack/repos/builtin/packages/elemental/package.py
+++ b/var/spack/repos/builtin/packages/elemental/package.py
@@ -36,8 +36,6 @@ class Elemental(CMakePackage):
     version('0.87.7', '6c1e7442021c59a36049e37ea69b8075')
     version('0.87.6', '9fd29783d45b0a0e27c0df85f548abe9')
 
-    variant('debug', default=False,
-            description='Builds a debug version of the libraries')
     variant('shared', default=True,
             description='Enables the build of shared libraries')
     variant('hybrid', default=True,
@@ -61,6 +59,9 @@ class Elemental(CMakePackage):
             ' Requires local build of BLAS library.')
     variant('scalapack', default=False,
             description='Build with ScaLAPACK library')
+    variant('build_type', default='Release',
+            description='The build type to build',
+            values=('Debug', 'Release'))
 
     # Note that this forces us to use OpenBLAS until #1712 is fixed
     depends_on('blas', when='~openmp_blas ~int64_blas')
@@ -85,15 +86,6 @@ def libs(self):
             'libEl', root=self.prefix, shared=shared, recurse=True
         )
 
-    def build_type(self):
-        """Returns the correct value for the ``CMAKE_BUILD_TYPE`` variable
-        :return: value for ``CMAKE_BUILD_TYPE``
-        """
-        if '+debug' in self.spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         spec = self.spec
 
diff --git a/var/spack/repos/builtin/packages/espressopp/package.py b/var/spack/repos/builtin/packages/espressopp/package.py
index e71291bec86..f1752b3b5eb 100644
--- a/var/spack/repos/builtin/packages/espressopp/package.py
+++ b/var/spack/repos/builtin/packages/espressopp/package.py
@@ -39,7 +39,6 @@ class Espressopp(CMakePackage):
     version('1.9.4.1', '0da74a6d4e1bfa6a2a24fca354245a4f')
     version('1.9.4', 'f2a27993a83547ad014335006eea74ea')
 
-    variant('debug', default=False, description='Build debug version')
     variant('ug', default=False, description='Build user guide')
     variant('pdf', default=False, description='Build user guide in pdf format')
     variant('dg', default=False, description='Build developer guide')
@@ -60,13 +59,6 @@ class Espressopp(CMakePackage):
     depends_on("texlive", when="+pdf", type='build')
     depends_on("doxygen", when="+dg", type='build')
 
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         return ['-DEXTERNAL_MPI4PY=ON', '-DEXTERNAL_BOOST=ON']
 
diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py
index 34afa0d609c..5aa3b17d73b 100644
--- a/var/spack/repos/builtin/packages/fenics/package.py
+++ b/var/spack/repos/builtin/packages/fenics/package.py
@@ -55,10 +55,12 @@ class Fenics(CMakePackage):
             description='Enables the shared memory support')
     variant('shared',       default=True,
             description='Enables the build of shared libraries')
-    variant('debug',        default=False,
-            description='Builds a debug version of the libraries')
     variant('doc',          default=False,
             description='Builds the documentation')
+    variant('build_type', default='RelWithDebInfo',
+            description='The build type to build',
+            values=('Debug', 'Release', 'RelWithDebInfo',
+                    'MinSizeRel', 'Developer'))
 
     # not part of spack list for now
     # variant('petsc4py',     default=True,  description='Uses PETSc4py')
@@ -144,11 +146,7 @@ def cmake_is_on(self, option):
         return 'ON' if option in self.spec else 'OFF'
 
     def cmake_args(self):
-        spec = self.spec
-
         return [
-            '-DCMAKE_BUILD_TYPE:STRING={0}'.format(
-                'Debug' if '+debug' in spec else 'RelWithDebInfo'),
             '-DDOLFIN_ENABLE_DOCS:BOOL={0}'.format(
                 self.cmake_is_on('+doc')),
             '-DBUILD_SHARED_LIBS:BOOL={0}'.format(
diff --git a/var/spack/repos/builtin/packages/flecsale/package.py b/var/spack/repos/builtin/packages/flecsale/package.py
index b22c553d2ab..828ff47d2fd 100644
--- a/var/spack/repos/builtin/packages/flecsale/package.py
+++ b/var/spack/repos/builtin/packages/flecsale/package.py
@@ -33,7 +33,6 @@ class Flecsale(CMakePackage):
 
     version('develop', git='https://github.com/laristra/flecsale', branch='master', submodules=True)
 
-    variant('debug', default=False, description='Build debug version')
     variant('mpi', default=True,
             description='Build on top of mpi conduit for mpi inoperability')
 
@@ -43,13 +42,6 @@ class Flecsale(CMakePackage):
     depends_on("python")
     depends_on("openssl")
 
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         options = [
             '-DENABLE_UNIT_TESTS=ON'
diff --git a/var/spack/repos/builtin/packages/flecsi/package.py b/var/spack/repos/builtin/packages/flecsi/package.py
index 5c0f51b2d18..3b079565cb6 100644
--- a/var/spack/repos/builtin/packages/flecsi/package.py
+++ b/var/spack/repos/builtin/packages/flecsi/package.py
@@ -41,7 +41,6 @@ class Flecsi(CMakePackage):
 
     version('develop', git='https://github.com/laristra/flecsi', branch='master', submodules=True)
 
-    variant('debug', default=False, description='Build debug version')
     variant('mpi', default=True,
             description='Build on top of mpi conduit for mpi inoperability')
 
@@ -49,13 +48,6 @@ class Flecsi(CMakePackage):
     depends_on("legion+shared", when='~mpi')
     depends_on("legion+shared+mpi", when='+mpi')
 
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         options = ['-DENABLE_UNIT_TESTS=ON']
 
diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py
index cb04d674812..95d3eb9d551 100644
--- a/var/spack/repos/builtin/packages/geant4/package.py
+++ b/var/spack/repos/builtin/packages/geant4/package.py
@@ -41,7 +41,6 @@ class Geant4(CMakePackage):
     version('10.01.p03', '4fb4175cc0dabcd517443fbdccd97439')
 
     variant('qt', default=True, description='Enable Qt support')
-    variant('debug', default=False, description='Build debug version')
 
     depends_on('cmake@3.5:', type='build')
 
@@ -54,13 +53,6 @@ class Geant4(CMakePackage):
     depends_on("xerces-c")
     depends_on("qt@4.8:", when="+qt")
 
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         spec = self.spec
 
diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py
index 3c9eff5619f..977bf6c3d67 100644
--- a/var/spack/repos/builtin/packages/gmsh/package.py
+++ b/var/spack/repos/builtin/packages/gmsh/package.py
@@ -46,8 +46,6 @@ class Gmsh(CMakePackage):
 
     variant('shared',      default=True,
             description='Enables the build of shared libraries')
-    variant('debug',       default=False,
-            description='Builds the library in debug mode')
     variant('mpi',         default=True,
             description='Builds MPI support for parser and solver')
     variant('fltk',        default=False,
@@ -128,9 +126,6 @@ def cmake_args(self):
             # Builds and installs static library
             options.append('-DENABLE_BUILD_LIB:BOOL=ON')
 
-        if '+debug' in spec:
-            options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
-
         if '+mpi' in spec:
             options.append('-DENABLE_MPI:BOOL=ON')
 
diff --git a/var/spack/repos/builtin/packages/gobject-introspection/package.py b/var/spack/repos/builtin/packages/gobject-introspection/package.py
index 44078d059e2..26e5da3d568 100644
--- a/var/spack/repos/builtin/packages/gobject-introspection/package.py
+++ b/var/spack/repos/builtin/packages/gobject-introspection/package.py
@@ -46,6 +46,9 @@ class GobjectIntrospection(Package):
     depends_on("flex", type="build")
     depends_on("pkg-config@0.9.0:", type="build")
 
+    # GobjectIntrospection does not build with sed from darwin:
+    depends_on('sed', when='platform=darwin', type='build')
+
     # This package creates several scripts from
     # toosl/g-ir-tool-template.in.  In their original form these
     # scripts end up with a sbang line like
diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py
index 97fd569d1ff..ae17193139c 100644
--- a/var/spack/repos/builtin/packages/gromacs/package.py
+++ b/var/spack/repos/builtin/packages/gromacs/package.py
@@ -48,12 +48,15 @@ class Gromacs(CMakePackage):
     variant('mpi', default=True, description='Activate MPI support')
     variant('shared', default=True,
             description='Enables the build of shared libraries')
-    variant('debug', default=False, description='Enables debug mode')
     variant(
         'double', default=False,
         description='Produces a double precision version of the executables')
     variant('plumed', default=False, description='Enable PLUMED support')
     variant('cuda', default=False, description='Enable CUDA support')
+    variant('build_type', default='RelWithDebInfo',
+            description='The build type to build',
+            values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel',
+                    'Reference', 'RelWithAssert', 'Profile'))
 
     depends_on('mpi', when='+mpi')
     depends_on('plumed+mpi', when='+plumed+mpi')
@@ -79,11 +82,6 @@ def cmake_args(self):
         if '~shared' in self.spec:
             options.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
 
-        if '+debug' in self.spec:
-            options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
-        else:
-            options.append('-DCMAKE_BUILD_TYPE:STRING=Release')
-
         if '+cuda' in self.spec:
             options.append('-DGMX_GPU:BOOL=ON')
             options.append('-DCUDA_TOOLKIT_ROOT_DIR:STRING=' +
diff --git a/var/spack/repos/builtin/packages/hpx/package.py b/var/spack/repos/builtin/packages/hpx/package.py
index ef7b347426c..58644db11e7 100644
--- a/var/spack/repos/builtin/packages/hpx/package.py
+++ b/var/spack/repos/builtin/packages/hpx/package.py
@@ -40,10 +40,3 @@ class Hpx(CMakePackage):
     def cmake_args(self):
         args = ['-DHPX_BUILD_EXAMPLES=OFF', '-DHPX_MALLOC=system']
         return args
-
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index a018529baef..249b03a74f8 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -48,6 +48,8 @@ class Jdk(Package):
     # For instructions on how to find the magic URL, see:
     # https://gist.github.com/P7h/9741922
     # https://linuxconfig.org/how-to-install-java-se-development-kit-on-debian-linux
+    version('8u141-b15', '8cf4c4e00744bfafc023d770cb65328c', curl_options=curl_options,
+            url='http://download.oracle.com/otn-pub/java/jdk/8u141-b15/336fa29ff2bb4ef291e347e091f7f4a7/jdk-8u141-linux-x64.tar.gz')
     version('8u131-b11', '75b2cb2249710d822a60f83e28860053', curl_options=curl_options,
             url='http://download.oracle.com/otn-pub/java/jdk/8u131-b11/d54c1d3a095b4ff2b6607d096fa80163/jdk-8u131-linux-x64.tar.gz')
     version('8u92-b14',  '65a1cc17ea362453a6e0eb4f13be76e4', curl_options=curl_options)
diff --git a/var/spack/repos/builtin/packages/lbann/package.py b/var/spack/repos/builtin/packages/lbann/package.py
index b79f9244c98..fea19245503 100644
--- a/var/spack/repos/builtin/packages/lbann/package.py
+++ b/var/spack/repos/builtin/packages/lbann/package.py
@@ -36,24 +36,16 @@ class Lbann(CMakePackage):
     version('develop', git='https://github.com/LLNL/lbann.git', branch="develop")
     version('0.91', '83b0ec9cd0b7625d41dfb06d2abd4134')
 
-    variant('debug', default=False, description='Builds a debug version of the libraries')
     variant('gpu', default=False, description='Builds with support for GPUs via CUDA and cuDNN')
     variant('opencv', default=True, description='Builds with support for image processing routines with OpenCV')
     variant('seq_init', default=False, description='Force serial initialization of weight matrices.')
 
     depends_on('elemental +openmp_blas +scalapack +shared +int64')
-    depends_on('elemental +openmp_blas +scalapack +shared +int64 +debug', when='+debug')
     depends_on('cuda', when='+gpu')
     depends_on('mpi')
     depends_on('opencv@3.2.0', when='+opencv')
     depends_on('protobuf@3.0.2:')
 
-    def build_type(self):
-        if '+debug' in self.spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         spec = self.spec
         # Environment variables
diff --git a/var/spack/repos/builtin/packages/legion/package.py b/var/spack/repos/builtin/packages/legion/package.py
index 79a1ee533d6..3bcd37e3068 100644
--- a/var/spack/repos/builtin/packages/legion/package.py
+++ b/var/spack/repos/builtin/packages/legion/package.py
@@ -46,7 +46,6 @@ class Legion(CMakePackage):
     version('develop', git='https://github.com/StanfordLegion/legion', branch='master')
     version('17.02.0', '31ac3004e2fb0996764362d2b6f6844a')
 
-    variant('debug', default=False, description='Build debug version')
     variant('mpi', default=True,
             description='Build on top of mpi conduit for mpi inoperability')
     variant('shared', default=True, description='Build shared libraries')
@@ -55,13 +54,6 @@ class Legion(CMakePackage):
     depends_on("gasnet", when='~mpi')
     depends_on("gasnet+mpi", when='+mpi')
 
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         options = [
             '-DLegion_USE_GASNet=ON',
diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index fc8823f1a81..64e50f0cfb7 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -43,10 +43,10 @@ class Llvm(CMakePackage):
     version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005',
             url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz')
 
-    variant('debug', default=False,
-            description="Build a debug version of LLVM, this increases "
-            "binary size by an order of magnitude, make sure you have "
-            "20-30gb of space available to build this")
+    # NOTE: The debug version of LLVM is an order of magnitude larger than
+    # the release version, and may take up 20-30 GB of space. If you want
+    # to save space, build with `build_type=Release`.
+
     variant('clang', default=True,
             description="Build the LLVM C/C++/Objective-C compiler frontend")
     variant('lldb', default=True, description="Build the LLVM debugger")
@@ -327,12 +327,6 @@ class Llvm(CMakePackage):
     def setup_environment(self, spack_env, run_env):
         spack_env.append_flags('CXXFLAGS', self.compiler.cxx11_flag)
 
-    def build_type(self):
-        if '+debug' in self.spec:
-            return 'RelWithDebInfo'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         spec = self.spec
 
diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py
index 0680e1a3b50..ecb2a8b5435 100644
--- a/var/spack/repos/builtin/packages/lua/package.py
+++ b/var/spack/repos/builtin/packages/lua/package.py
@@ -145,11 +145,11 @@ def setup_environment(self, spack_env, run_env):
 
     @property
     def lua_lib_dir(self):
-        return os.path.join('lib', 'lua', self.version.up_to(2))
+        return os.path.join('lib', 'lua', str(self.version.up_to(2)))
 
     @property
     def lua_share_dir(self):
-        return os.path.join('share', 'lua', self.version.up_to(2))
+        return os.path.join('share', 'lua', str(self.version.up_to(2)))
 
     def setup_dependent_package(self, module, dependent_spec):
         """
diff --git a/var/spack/repos/builtin/packages/mad-numdiff/package.py b/var/spack/repos/builtin/packages/mad-numdiff/package.py
index 4d0c9c1ef73..574ddf2be37 100644
--- a/var/spack/repos/builtin/packages/mad-numdiff/package.py
+++ b/var/spack/repos/builtin/packages/mad-numdiff/package.py
@@ -34,12 +34,3 @@ class MadNumdiff(CMakePackage):
 
     version('develop', git='https://github.com/quinoacomputing/ndiff', branch='master')
     version('20150724', '7723c0f2499aea8fd960377c5bed28d8')
-
-    variant('debug', default=False, description='Build debug version')
-
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py
index d69dedf3eaf..33a6bb5640d 100644
--- a/var/spack/repos/builtin/packages/magics/package.py
+++ b/var/spack/repos/builtin/packages/magics/package.py
@@ -109,7 +109,7 @@ def install(self, spec, prefix):
         if '+metview' in spec:
             if '+qt' in spec:
                 options.append('-DENABLE_METVIEW=ON')
-                if spec['qt'].version.up_to(1) == '5':
+                if spec['qt'].version[0] == 5:
                     options.append('-DENABLE_QT5=ON')
             else:
                 options.append('-DENABLE_METVIEW_NO_QT=ON')
diff --git a/var/spack/repos/builtin/packages/nalu/package.py b/var/spack/repos/builtin/packages/nalu/package.py
index fc6d79e9ea0..040144ff164 100644
--- a/var/spack/repos/builtin/packages/nalu/package.py
+++ b/var/spack/repos/builtin/packages/nalu/package.py
@@ -38,19 +38,10 @@ class Nalu(CMakePackage):
     version('master',
             git='https://github.com/NaluCFD/Nalu.git', branch='master')
 
-    variant('debug', default=False,
-            description='Builds a debug version')
-
     # Currently Nalu only builds static libraries; To be fixed soon
     depends_on('yaml-cpp+fpic~shared')
     depends_on('trilinos~shared+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf@master')
 
-    def build_type(self):
-        if '+debug' in self.spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         spec = self.spec
         options = []
diff --git a/var/spack/repos/builtin/packages/nekbone/package.py b/var/spack/repos/builtin/packages/nekbone/package.py
index 7d2b61f038c..22d07661e5f 100644
--- a/var/spack/repos/builtin/packages/nekbone/package.py
+++ b/var/spack/repos/builtin/packages/nekbone/package.py
@@ -39,6 +39,8 @@ class Nekbone(Package):
 
     version('develop', git='https://github.com/ANL-CESAR/nekbone.git')
 
+    depends_on('mpi')
+
     def install(self, spec, prefix):
 
         working_dirs = ['example1', 'example2', 'example3', 'nek_comm',
@@ -47,6 +49,9 @@ def install(self, spec, prefix):
 
         for wdir in working_dirs:
             with working_dir('test/' + wdir):
+                makenec = FileFilter('makenek')
+                makenec.filter('CC.*', 'CC=' + self.spec['mpi'].mpicc)
+                makenec.filter('FF77.*', 'FF77=' + self.spec['mpi'].mpif77)
                 makenek = Executable('./makenek')
                 path = join_path(prefix.bin,  wdir)
                 makenek('ex1', '../../src')
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index d79e2c27f8d..5afbd1e325d 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -33,6 +33,7 @@ class Openblas(MakefilePackage):
     homepage = 'http://www.openblas.net'
     url = 'http://github.com/xianyi/OpenBLAS/archive/v0.2.19.tar.gz'
 
+    version('0.2.20', '48637eb29f5b492b91459175dcc574b1')
     version('0.2.19', '28c998054fd377279741c6f0b9ea7941')
     version('0.2.18', '805e7f660877d588ea7e3792cda2ee65')
     version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1')
diff --git a/var/spack/repos/builtin/packages/opencoarrays/package.py b/var/spack/repos/builtin/packages/opencoarrays/package.py
index 0449155bc7f..37ae236c0ad 100644
--- a/var/spack/repos/builtin/packages/opencoarrays/package.py
+++ b/var/spack/repos/builtin/packages/opencoarrays/package.py
@@ -42,6 +42,11 @@ class Opencoarrays(CMakePackage):
     version('1.7.4', '85ba87def461e3ff5a164de2e6482930')
     version('1.6.2', '5a4da993794f3e04ea7855a6678981ba')
 
+    variant('build_type', default='RelWithDebInfo',
+            description='The build type to build',
+            values=('Debug', 'Release', 'RelWithDebInfo',
+                    'MinSizeRel', 'CodeCoverage'))
+
     depends_on('mpi')
 
     def cmake_args(self):
diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py
index a86465b1ba8..95971af10e0 100644
--- a/var/spack/repos/builtin/packages/openspeedshop/package.py
+++ b/var/spack/repos/builtin/packages/openspeedshop/package.py
@@ -149,9 +149,6 @@ class Openspeedshop(CMakePackage):
 
     build_directory = 'build_openspeedshop'
 
-    def build_type(self):
-        return 'None'
-
     def cmake_args(self):
         spec = self.spec
         compile_flags = "-O2 -g"
diff --git a/var/spack/repos/builtin/packages/pegtl/package.py b/var/spack/repos/builtin/packages/pegtl/package.py
index 85a008a1199..f6848be725a 100644
--- a/var/spack/repos/builtin/packages/pegtl/package.py
+++ b/var/spack/repos/builtin/packages/pegtl/package.py
@@ -39,12 +39,3 @@ class Pegtl(CMakePackage):
     version('develop', git='https://github.com/taocpp/PEGTL', branch='master')
     version('2.1.4', 'e5288b6968e6e910287fce93dc5557bf')
     version('2.0.0', 'c772828e7188459338a920c21f9896db')
-
-    variant('debug', default=False, description='Build debug version')
-
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
diff --git a/var/spack/repos/builtin/packages/perl-math-cdf/package.py b/var/spack/repos/builtin/packages/perl-math-cdf/package.py
new file mode 100644
index 00000000000..6d7d195dea6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-math-cdf/package.py
@@ -0,0 +1,35 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PerlMathCdf(PerlPackage):
+    """Generate probabilities and quantiles from several statistical
+       probability functions"""
+
+    homepage = "http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/Math-CDF-0.1.tar.gz"
+
+    version('0.1', '7866c7b6b9d27f0ce4b7637334478ab7')
diff --git a/var/spack/repos/builtin/packages/portage/package.py b/var/spack/repos/builtin/packages/portage/package.py
index 92e42665523..0934076ab90 100644
--- a/var/spack/repos/builtin/packages/portage/package.py
+++ b/var/spack/repos/builtin/packages/portage/package.py
@@ -36,19 +36,11 @@ class Portage(CMakePackage):
 
     version('develop', git='https://github.com/laristra/portage', branch='master', submodules=True)
 
-    variant('debug', default=False, description='Build debug version')
     variant('mpi', default=True, description='Support MPI')
 
     depends_on("cmake@3.1:", type='build')
     depends_on('mpi', when='+mpi')
 
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         options = ['-DENABLE_UNIT_TESTS=ON', '-DENABLE_APP_TESTS=ON']
 
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 551f87b5d78..89e821b68f8 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -131,9 +131,9 @@ def url_for_version(self, version):
         url = self.list_url
 
         if version >= Version('4.0'):
-            url += version.up_to(2) + '/'
+            url += str(version.up_to(2)) + '/'
         else:
-            url += version.up_to(1) + '/'
+            url += str(version.up_to(1)) + '/'
 
         if version >= Version('4.8'):
             url += str(version) + '/'
diff --git a/var/spack/repos/builtin/packages/quinoa/package.py b/var/spack/repos/builtin/packages/quinoa/package.py
index eb41bb8b371..de04e6407cd 100644
--- a/var/spack/repos/builtin/packages/quinoa/package.py
+++ b/var/spack/repos/builtin/packages/quinoa/package.py
@@ -38,8 +38,6 @@ class Quinoa(CMakePackage):
 
     version('develop', git='https://github.com/quinoacomputing/quinoa', branch='master')
 
-    variant('debug', default=False, description='Build debug version')
-
     depends_on('hdf5+mpi')
     depends_on("charm backend=mpi")
     depends_on("trilinos+exodus")
@@ -56,10 +54,3 @@ class Quinoa(CMakePackage):
     depends_on("pegtl")
 
     root_cmakelists_dir = 'src'
-
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
diff --git a/var/spack/repos/builtin/packages/relion/package.py b/var/spack/repos/builtin/packages/relion/package.py
index dfb93cd9434..23b1834fbc7 100644
--- a/var/spack/repos/builtin/packages/relion/package.py
+++ b/var/spack/repos/builtin/packages/relion/package.py
@@ -40,6 +40,10 @@ class Relion(CMakePackage):
     variant('cuda', default=False, description="enable compute on gpu")
     variant('double', default=False, description="double precision (cpu) code")
     variant('double-gpu', default=False, description="double precision (gpu) code")
+    variant('build_type', default='RelWithDebInfo',
+            description='The build type to build',
+            values=('Debug', 'Release', 'RelWithDebInfo',
+                    'Profiling', 'Benchmarking'))
 
     depends_on('mpi')
     depends_on('fftw+float+double')
diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py
index b5f6ce89fe9..dfd7ba3e25a 100644
--- a/var/spack/repos/builtin/packages/root/package.py
+++ b/var/spack/repos/builtin/packages/root/package.py
@@ -99,12 +99,6 @@ class Root(CMakePackage):
     # See https://sft.its.cern.ch/jira/browse/ROOT-7517
     conflicts('%intel')
 
-    def build_type(self):
-        if '+debug' in self.spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         args = [
             '-Dcocoa=OFF',
diff --git a/var/spack/repos/builtin/packages/sas/package.py b/var/spack/repos/builtin/packages/sas/package.py
index 5a7f1de1d5d..050d6172d65 100644
--- a/var/spack/repos/builtin/packages/sas/package.py
+++ b/var/spack/repos/builtin/packages/sas/package.py
@@ -36,19 +36,10 @@ class Sas(CMakePackage):
     version('0.1.4', '20d7311258f2a59c9367ae1576c392b6')
     version('0.1.3', '1e6572afcc03318d16d7321d40eec0fd')
 
-    variant('debug', default=False, description='Build debug version')
-
     depends_on('python@2.7:')
     depends_on('llvm@3.5:')
     depends_on('cmake@2.8:', type='build')
 
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         args = [
             '-DLLVM_DEV_DIR=%s' % self.spec['llvm'].prefix
diff --git a/var/spack/repos/builtin/packages/shortstack/package.py b/var/spack/repos/builtin/packages/shortstack/package.py
new file mode 100644
index 00000000000..8feb6710139
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shortstack/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Shortstack(Package):
+    """ShortStack is a tool developed to process and analyze smallRNA-seq data
+       with respect to a reference genome, and output a comprehensive and
+       informative annotation of all discovered small RNA genes."""
+
+    homepage = "http://sites.psu.edu/axtell/software/shortstack/"
+    url      = "https://github.com/MikeAxtell/ShortStack/archive/v3.8.3.tar.gz"
+
+    version('3.8.3', '3f21f494f799039f3fa88ea343f2d20d')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('samtools')
+    depends_on('viennarna')
+    depends_on('bowtie')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('ShortStack', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/snptest/package.py b/var/spack/repos/builtin/packages/snptest/package.py
new file mode 100644
index 00000000000..a60a15d0548
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snptest/package.py
@@ -0,0 +1,39 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Snptest(Package):
+    """SNPTEST is a program for the analysis of single SNP association in
+       genome-wide studies."""
+
+    homepage = "https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html"
+    url = "http://www.well.ox.ac.uk/~gav/resources/snptest_v2.5.2_linux_x86_64_dynamic.tgz"
+
+    version('2.5.2', 'e3f2cc0351f260cf29369dc4f79a660a')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('snptest_v{0}'.format(self.version), prefix.bin)
diff --git a/var/spack/repos/builtin/packages/stacks/package.py b/var/spack/repos/builtin/packages/stacks/package.py
new file mode 100644
index 00000000000..df0d486b0ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/stacks/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Stacks(AutotoolsPackage):
+    """Stacks is a software pipeline for building loci from short-read
+       sequences, such as those generated on the Illumina platform."""
+
+    homepage = "http://catchenlab.life.illinois.edu/stacks/"
+    url      = "http://catchenlab.life.illinois.edu/stacks/source/stacks-1.46.tar.gz"
+
+    version('1.46', '18b0568a4bba44fb4e5be0eb7ee2c08d')
+
+    variant('sparsehash', default=True, description='Improve Stacks memory usage with SparseHash')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('sparsehash', when='+sparsehash')
+
+    def configure_args(self):
+        args = []
+        if '+sparsehash' in self.spec:
+            args.append('--enable-sparsehash')
+        else:
+            args.append('--disable-sparsehash')
+        return args
diff --git a/var/spack/repos/builtin/packages/stringtie/package.py b/var/spack/repos/builtin/packages/stringtie/package.py
new file mode 100644
index 00000000000..9baf545a4c7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/stringtie/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Stringtie(MakefilePackage):
+    """StringTie is a fast and highly efficient assembler of RNA-Seq alignments
+       into potential transcripts."""
+
+    homepage = "https://ccb.jhu.edu/software/stringtie"
+    url      = "https://github.com/gpertea/stringtie/archive/v1.3.3b.tar.gz"
+
+    version('1.3.3b', '11a43260b18e4272182380e922445d88')
+
+    depends_on('samtools')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('stringtie', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/structure/package.py b/var/spack/repos/builtin/packages/structure/package.py
new file mode 100644
index 00000000000..abe1ee76e88
--- /dev/null
+++ b/var/spack/repos/builtin/packages/structure/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Structure(MakefilePackage):
+    """Structure is a free software package for using multi-locus genotype
+       data to investigate population structure."""
+
+    homepage = "http://web.stanford.edu/group/pritchardlab/structure.html"
+    url      = "http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/structure_kernel_source.tar.gz"
+
+    version('2.3.4', '4e0591678cdbfe79347d272b5dceeda1')
+
+    depends_on('jdk', type=('build', 'run'))
+
+    def url_for_version(self, version):
+        url = "http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v{0}/structure_kernel_source.tar.gz"
+        return url.format(version)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('structure', prefix.bin)
+        install('mainparams', prefix.bin)
+        install('extraparams', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/sublime-text/package.py b/var/spack/repos/builtin/packages/sublime-text/package.py
index 3d7fb65005d..e7605b40be2 100644
--- a/var/spack/repos/builtin/packages/sublime-text/package.py
+++ b/var/spack/repos/builtin/packages/sublime-text/package.py
@@ -49,7 +49,7 @@ class SublimeText(Package):
     depends_on('libxau', type='run')
 
     def url_for_version(self, version):
-        if version.up_to(1) == '2':
+        if version[0] == 2:
             return "https://download.sublimetext.com/Sublime%20Text%20{0}%20x64.tar.bz2".format(version)
         else:
             return "https://download.sublimetext.com/sublime_text_3_build_{0}_x64.tar.bz2".format(version)
diff --git a/var/spack/repos/builtin/packages/subread/package.py b/var/spack/repos/builtin/packages/subread/package.py
new file mode 100644
index 00000000000..b09e3986024
--- /dev/null
+++ b/var/spack/repos/builtin/packages/subread/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import sys
+
+
+class Subread(MakefilePackage):
+    """The Subread software package is a tool kit for processing next-gen
+       sequencing data."""
+
+    homepage = "http://subread.sourceforge.net/"
+    url      = "https://downloads.sourceforge.net/project/subread/subread-1.5.2/subread-1.5.2-source.tar.gz"
+
+    version('1.5.2', '817d2a46d87fcef885c8832475b8b247')
+
+    depends_on('zlib')
+
+    def build(self, spec, prefix):
+        plat = sys.platform
+        with working_dir('src'):
+            if plat.startswith('linux'):
+                make('-f', 'Makefile.Linux')
+            elif plat.startswith('darwin'):
+                make('-f', 'Makefile.MacOS')
+            else:
+                raise InstallError("The communication mechanism %s is not"
+                                   "supported" % plat)
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/sumaclust/package.py b/var/spack/repos/builtin/packages/sumaclust/package.py
new file mode 100644
index 00000000000..b1d7a94c5a1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sumaclust/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Sumaclust(MakefilePackage):
+    """Sumaclust aims to cluster sequences in a way that is fast and exact at
+       the same time."""
+
+    homepage = "https://git.metabarcoding.org/obitools/sumaclust"
+
+    version('1.0.20', '31c7583fbe2e3345d5fe3e9431d9b30c',
+            url="https://git.metabarcoding.org/obitools/sumaclust/uploads/69f757c42f2cd45212c587e87c75a00f/sumaclust_v1.0.20.tar.gz")
+
+    def build(self, spec, prefix):
+        make('CC={0}'.format(spack_cc))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('sumaclust', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/swarm/package.py b/var/spack/repos/builtin/packages/swarm/package.py
new file mode 100644
index 00000000000..b752f523813
--- /dev/null
+++ b/var/spack/repos/builtin/packages/swarm/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Swarm(MakefilePackage):
+    """A robust and fast clustering method for amplicon-based studies."""
+
+    homepage = "https://github.com/torognes/swarm"
+    url      = "https://github.com/torognes/swarm/archive/v2.1.13.tar.gz"
+
+    version('2.1.13', 'ab6aff0ba5d20a53b9f13f8f3d85839f')
+
+    build_directory = 'src'
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('scripts', prefix.scripts)
+        install_tree('man', prefix.share.man)
diff --git a/var/spack/repos/builtin/packages/symengine/package.py b/var/spack/repos/builtin/packages/symengine/package.py
index 50dd335ac70..a36cfc70b2b 100644
--- a/var/spack/repos/builtin/packages/symengine/package.py
+++ b/var/spack/repos/builtin/packages/symengine/package.py
@@ -55,6 +55,9 @@ class Symengine(CMakePackage):
             description='Enable thread safety option')
     variant('shared',       default=True,
             description='Enables the build of shared libraries')
+    variant('build_type', default='Release',
+            description='The build type to build',
+            values=('Debug', 'Release'))
 
     # NOTE: mpir is a drop-in replacement for gmp
     # NOTE: [mpc,mpfr,flint,piranha] could also be built against mpir
@@ -66,10 +69,6 @@ class Symengine(CMakePackage):
     depends_on('flint',    when='+flint~boostmp')
     depends_on('piranha',  when='+piranha~flint~boostmp')
 
-    def build_type(self):
-        # CMAKE_BUILD_TYPE should be  Debug | Release
-        return 'Release'
-
     def cmake_args(self):
         spec = self.spec
         options = []
@@ -77,7 +76,6 @@ def cmake_args(self):
         # See https://github.com/symengine/symengine/blob/master/README.md
         # for build options
         options.extend([
-            '-DCMAKE_BUILD_TYPE=Release',
             '-DWITH_SYMENGINE_RCP:BOOL=ON',
             '-DWITH_SYMENGINE_THREAD_SAFE:BOOL=%s' % (
                 'ON' if ('+thread_safe' or '+openmp') in spec else 'OFF'),
diff --git a/var/spack/repos/builtin/packages/tabix/package.py b/var/spack/repos/builtin/packages/tabix/package.py
new file mode 100644
index 00000000000..1e54dd4716b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tabix/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Tabix(MakefilePackage):
+    """Generic indexer for TAB-delimited genome position files"""
+
+    homepage = "https://github.com/samtools/tabix"
+    url      = "https://github.com/samtools/tabix"
+
+    version('2013-12-16', git='https://github.com/samtools/tabix.git', commit='1ae158ac79b459f5feeed7490c67519b14ce9f35')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('python', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        mkdirp(prefix.share.man.man1)
+        install('tabix', prefix.bin)
+        install('bgzip', prefix.bin)
+        install('tabix.py', prefix.bin)
+        install('tabix.1', prefix.share.man.man1)
+        install('tabix.tex', prefix.share)
+        install('TabixReader.java', prefix.bin)
+        install('libtabix.a', prefix.lib)
+        install_tree('perl', prefix.perl)
+        install_tree('python', prefix.python)
diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py
index 63d6c943b8e..a3a8e5ad891 100644
--- a/var/spack/repos/builtin/packages/tmux/package.py
+++ b/var/spack/repos/builtin/packages/tmux/package.py
@@ -25,7 +25,7 @@
 from spack import *
 
 
-class Tmux(Package):
+class Tmux(AutotoolsPackage):
     """Tmux is a terminal multiplexer.
 
     What is a terminal multiplexer? It lets you switch easily between several
@@ -45,15 +45,5 @@ class Tmux(Package):
     depends_on('libevent')
     depends_on('ncurses')
 
-    def install(self, spec, prefix):
-        pkg_config_path = ':'.join([
-            spec['libevent'].prefix,
-            spec['ncurses'].prefix
-        ])
-
-        configure(
-            "--prefix=%s" % prefix,
-            "PKG_CONFIG_PATH=%s" % pkg_config_path)
-
-        make()
-        make("install")
+    def configure_args(self):
+        return ['LIBTINFO_LIBS=-lncurses']
diff --git a/var/spack/repos/builtin/packages/transdecoder/package.py b/var/spack/repos/builtin/packages/transdecoder/package.py
new file mode 100644
index 00000000000..4c23afbf2a2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/transdecoder/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Transdecoder(MakefilePackage):
+    """TransDecoder identifies candidate coding regions within transcript
+       sequences, such as those generated by de novo RNA-Seq transcript
+       assembly using Trinity, or constructed based on RNA-Seq alignments to
+       the genome using Tophat and Cufflinks."""
+
+    homepage = "http://transdecoder.github.io/"
+    url      = "https://github.com/TransDecoder/TransDecoder/archive/v3.0.1.tar.gz"
+
+    version('3.0.1', 'f62b86a15fcb78b1dada9f80cc25f300')
+
+    depends_on('perl', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('TransDecoder.LongOrfs', prefix)
+        install('TransDecoder.Predict', prefix)
+        install_tree('PerlLib', prefix.PerlLib)
+        install_tree('util', prefix.util)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', prefix.util.bin)
+        run_env.prepend_path('PATH', prefix)
diff --git a/var/spack/repos/builtin/packages/transposome/package.py b/var/spack/repos/builtin/packages/transposome/package.py
new file mode 100644
index 00000000000..01499290cfd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/transposome/package.py
@@ -0,0 +1,37 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Transposome(PerlPackage):
+    """A toolkit for annotation of transposable element families from
+       unassembled sequence reads."""
+
+    homepage = "https://sestaton.github.io/Transposome/"
+    url      = "https://github.com/sestaton/Transposome/archive/v0.11.2.tar.gz"
+
+    version('0.11.2', '157c1fc090b0aa30050d03df885dcde0')
+
+    depends_on('blast-plus')
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 74022f08331..8566adc6491 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -93,8 +93,6 @@ class Trilinos(CMakePackage):
             description='Build python wrappers')
     variant('shared',       default=True,
             description='Enables the build of shared libraries')
-    variant('debug',        default=False,
-            description='Builds a debug version of the libraries')
     variant('boost',        default=True,
             description='Compile with Boost')
     variant('tpetra',       default=True,
@@ -241,8 +239,6 @@ def cmake_args(self):
             '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
             '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
             '-DTrilinos_ENABLE_CXX11:BOOL=ON',
-            '-DCMAKE_BUILD_TYPE:STRING=%s' % (
-                'DEBUG' if '+debug' in spec else 'RELEASE'),
             '-DBUILD_SHARED_LIBS:BOOL=%s' % (
                 'ON' if '+shared' in spec else 'OFF'),
 
diff --git a/var/spack/repos/builtin/packages/trimgalore/package.py b/var/spack/repos/builtin/packages/trimgalore/package.py
new file mode 100644
index 00000000000..9dd8be11e95
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trimgalore/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Trimgalore(Package):
+    """Trim Galore! is a wrapper around Cutadapt and FastQC to consistently
+       apply adapter and quality trimming to FastQ files, with extra
+       functionality for RRBS data."""
+
+    homepage = "https://github.com/FelixKrueger/TrimGalore"
+    url      = "https://github.com/FelixKrueger/TrimGalore/archive/0.4.4.tar.gz"
+
+    version('0.4.4', 'aae1b807b48e38bae7074470203997bb')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('py-cutadapt', type=('build', 'run'))
+    depends_on('fastqc')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('trim_galore', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/vc/package.py b/var/spack/repos/builtin/packages/vc/package.py
index e41a385947c..67ced036b25 100644
--- a/var/spack/repos/builtin/packages/vc/package.py
+++ b/var/spack/repos/builtin/packages/vc/package.py
@@ -35,11 +35,7 @@ class Vc(CMakePackage):
     version('1.2.0', 'a5236df286b845d2fee5ef1e4d27549f')
     version('1.1.0', 'e354c1e3ea1d674b6f2af9c6fd230d81')
 
-    variant('debug', default=False)
-
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
+    variant('build_type', default='RelWithDebInfo',
+            description='The build type to build',
+            values=('Debug', 'Release', 'RelWithDebug',
+                    'RelWithDebInfo', 'MinSizeRel'))
diff --git a/var/spack/repos/builtin/packages/vecgeom/package.py b/var/spack/repos/builtin/packages/vecgeom/package.py
index d514f13c174..9843840e5b0 100644
--- a/var/spack/repos/builtin/packages/vecgeom/package.py
+++ b/var/spack/repos/builtin/packages/vecgeom/package.py
@@ -36,17 +36,8 @@ class Vecgeom(CMakePackage):
     version('0.3.rc', git='https://gitlab.cern.ch/VecGeom/VecGeom.git',
             tag='v0.3.rc')
 
-    variant('debug', default=False, description='Build debug version')
-
     depends_on('cmake@3.5:', type='build')
 
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         options = [
             '-DBACKEND=Scalar',
diff --git a/var/spack/repos/builtin/packages/viennarna/package.py b/var/spack/repos/builtin/packages/viennarna/package.py
new file mode 100644
index 00000000000..548aacb56f0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/viennarna/package.py
@@ -0,0 +1,67 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Viennarna(AutotoolsPackage):
+    """The ViennaRNA Package consists of a C code library and several
+       stand-alone programs for the prediction and comparison of RNA secondary
+       structures."""
+
+    homepage = "https://www.tbi.univie.ac.at/RNA/"
+    url      = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/ViennaRNA-2.3.5.tar.gz"
+
+    version('2.3.5', '4542120adae9b7abb605e2304c2a1326')
+
+    variant('sse', default=True, description='Enable SSE in order to substantially speed up execution')
+    variant('perl', default=True, description='Build ViennaRNA with Perl interface')
+    variant('python', default=True, description='Build ViennaRNA with Python interface')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('python', type=('build', 'run'))
+    depends_on('libsvm')
+    depends_on('gsl')
+
+    def url_for_version(self, version):
+        url = 'https://www.tbi.univie.ac.at/RNA/download/sourcecode/{0}_x/ViennaRNA-{1}.tar.gz'
+        return url.format(version.up_to(2).underscored, version)
+
+    def configure_args(self):
+        args = []
+        if '+sse' in self.spec:
+            args.append('--enable-sse')
+        else:
+            args.append('--disable-sse')
+        if '~python' in self.spec:
+            args.append('--without-python')
+        else:
+            args.append('--with-python')
+        if '~perl' in self.spec:
+            args.append('--without-perl')
+        else:
+            args.append('--with-perl')
+        if 'python@3:' in self.spec:
+            args.append('--with-python3')
+        return args
diff --git a/var/spack/repos/builtin/packages/votca-csg/package.py b/var/spack/repos/builtin/packages/votca-csg/package.py
index 6756d0427b7..bd5879e68a0 100644
--- a/var/spack/repos/builtin/packages/votca-csg/package.py
+++ b/var/spack/repos/builtin/packages/votca-csg/package.py
@@ -39,16 +39,7 @@ class VotcaCsg(CMakePackage):
     version('develop', git='https://github.com/votca/csg', branch='master')
     version('1.4', 'd009e761e5e3afd51eed89c420610a67')
 
-    variant('debug', default=False, description='Build debug version')
-
     depends_on("cmake@2.8:", type='build')
     depends_on("votca-tools@1.4:1.4.999", when='@1.4:1.4.999')
     depends_on("votca-tools@develop", when='@develop')
     depends_on("gromacs~mpi@5.1:")
-
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
diff --git a/var/spack/repos/builtin/packages/votca-ctp/package.py b/var/spack/repos/builtin/packages/votca-ctp/package.py
index 81586b18e64..8ace1804873 100644
--- a/var/spack/repos/builtin/packages/votca-ctp/package.py
+++ b/var/spack/repos/builtin/packages/votca-ctp/package.py
@@ -39,16 +39,7 @@ class VotcaCtp(CMakePackage):
 
     version('develop', git='https://github.com/votca/ctp', branch='master')
 
-    variant('debug', default=False, description='Build debug version')
-
     depends_on("cmake@2.8:", type='build')
     depends_on("votca-tools@develop", when='@develop')
     depends_on("votca-csg@develop", when='@develop')
     depends_on("votca-moo@develop", when='@develop')
-
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
diff --git a/var/spack/repos/builtin/packages/votca-moo/package.py b/var/spack/repos/builtin/packages/votca-moo/package.py
index a596ba1c9c4..dfbef140eb1 100644
--- a/var/spack/repos/builtin/packages/votca-moo/package.py
+++ b/var/spack/repos/builtin/packages/votca-moo/package.py
@@ -39,14 +39,5 @@ class VotcaMoo(CMakePackage):
 
     version('develop', git='https://github.com/votca/moo', branch='master')
 
-    variant('debug', default=False, description='Build debug version')
-
     depends_on("cmake@2.8:", type='build')
     depends_on("votca-tools@develop", when='@develop')
-
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
diff --git a/var/spack/repos/builtin/packages/votca-tools/package.py b/var/spack/repos/builtin/packages/votca-tools/package.py
index 39055c45a3e..d2acac87369 100644
--- a/var/spack/repos/builtin/packages/votca-tools/package.py
+++ b/var/spack/repos/builtin/packages/votca-tools/package.py
@@ -39,18 +39,9 @@ class VotcaTools(CMakePackage):
     version('develop', git='https://github.com/votca/tools', branch='master')
     version('1.4', 'cd47868e9f28e2c7b9d01f95aa0185ca')
 
-    variant('debug', default=False, description='Build debug version')
-
     depends_on("cmake@2.8:", type='build')
     depends_on("expat")
     depends_on("fftw")
     depends_on("gsl")
     depends_on("boost")
     depends_on("sqlite")
-
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
diff --git a/var/spack/repos/builtin/packages/votca-xtp/package.py b/var/spack/repos/builtin/packages/votca-xtp/package.py
index 951df7b8c6a..80cd4802e38 100644
--- a/var/spack/repos/builtin/packages/votca-xtp/package.py
+++ b/var/spack/repos/builtin/packages/votca-xtp/package.py
@@ -39,17 +39,8 @@ class VotcaXtp(CMakePackage):
 
     version('develop', git='https://github.com/votca/xtp', branch='master')
 
-    variant('debug', default=False, description='Build debug version')
-
     depends_on("cmake@2.8:", type='build')
     depends_on("votca-tools@develop", when='@develop')
     depends_on("votca-csg@develop", when='@develop')
     depends_on("votca-ctp@develop", when='@develop')
     depends_on("votca-moo@develop", when='@develop')
-
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
diff --git a/var/spack/repos/builtin/packages/vpic/package.py b/var/spack/repos/builtin/packages/vpic/package.py
index e24aa9e5306..43083d813e0 100644
--- a/var/spack/repos/builtin/packages/vpic/package.py
+++ b/var/spack/repos/builtin/packages/vpic/package.py
@@ -40,18 +40,9 @@ class Vpic(CMakePackage):
 
     version('develop', git='https://github.com/lanl/vpic', branch='master', submodules=True)
 
-    variant('debug', default=False, description='Build debug version')
-
     depends_on("cmake@3.1:", type='build')
     depends_on('mpi')
 
-    def build_type(self):
-        spec = self.spec
-        if '+debug' in spec:
-            return 'Debug'
-        else:
-            return 'Release'
-
     def cmake_args(self):
         options = ['-DENABLE_INTEGRATED_TESTS=ON', '-DENABLE_UNIT_TESTS=ON']
 
diff --git a/var/spack/repos/builtin/packages/xsdktrilinos/package.py b/var/spack/repos/builtin/packages/xsdktrilinos/package.py
index 0d70baabcd1..cf3d425313c 100644
--- a/var/spack/repos/builtin/packages/xsdktrilinos/package.py
+++ b/var/spack/repos/builtin/packages/xsdktrilinos/package.py
@@ -45,20 +45,18 @@ class Xsdktrilinos(CMakePackage):
             description='Compile with PETSc solvers')
     variant('shared',       default=True,
             description='Enables the build of shared libraries')
-    variant('debug',        default=False,
-            description='Builds a debug version of the libraries')
 
     # MPI related dependencies
     depends_on('mpi')
     depends_on('hypre~internal-superlu', when='+hypre')
     depends_on('hypre@xsdk-0.2.0~internal-superlu', when='@xsdk-0.2.0+hypre')
-    depends_on('hypre@develop~internal-superlu', when='@develop+hypre')    
+    depends_on('hypre@develop~internal-superlu', when='@develop+hypre')
     depends_on('petsc@xsdk-0.2.0+mpi~complex', when='@xsdk-0.2.0+petsc')
-    depends_on('petsc@develop+mpi~complex', when='@develop+petsc')    
+    depends_on('petsc@develop+mpi~complex', when='@develop+petsc')
     depends_on('trilinos@12.6.4', when='@12.6.4')
     depends_on('trilinos@12.8.1', when='@12.8.1')
     depends_on('trilinos@xsdk-0.2.0', when='@xsdk-0.2.0')
-    depends_on('trilinos@develop', when='@develop')    
+    depends_on('trilinos@develop', when='@develop')
 
     def url_for_version(self, version):
         url = "https://github.com/trilinos/xSDKTrilinos/archive/trilinos-release-{0}.tar.gz"
@@ -75,8 +73,6 @@ def cmake_args(self):
             '-DxSDKTrilinos_ENABLE_TESTS:BOOL=ON',
             '-DxSDKTrilinos_ENABLE_EXAMPLES:BOOL=ON',
             '-DTrilinos_INSTALL_DIR=%s' % spec['trilinos'].prefix,
-            '-DCMAKE_BUILD_TYPE:STRING=%s' % (
-                'DEBUG' if '+debug' in spec else 'RELEASE'),
             '-DBUILD_SHARED_LIBS:BOOL=%s' % (
                 'ON' if '+shared' in spec else 'OFF'),
             '-DTPL_ENABLE_MPI:BOOL=ON',
diff --git a/var/spack/repos/builtin/packages/zstd/package.py b/var/spack/repos/builtin/packages/zstd/package.py
index 7cd5d6785d7..0551ff81631 100644
--- a/var/spack/repos/builtin/packages/zstd/package.py
+++ b/var/spack/repos/builtin/packages/zstd/package.py
@@ -25,7 +25,7 @@
 from spack import *
 
 
-class Zstd(Package):
+class Zstd(MakefilePackage):
     """Zstandard, or zstd as short version, is a fast lossless compression
     algorithm, targeting real-time compression scenarios at zlib-level and
     better compression ratios."""
@@ -33,10 +33,8 @@ class Zstd(Package):
     homepage = "http://facebook.github.io/zstd/"
     url      = "https://github.com/facebook/zstd/archive/v1.1.2.tar.gz"
 
+    version('1.3.0', '888660a850e33c2dcc7c4f9d0b04d347')
     version('1.1.2', '4c57a080d194bdaac83f2d3251fc7ffc')
 
     def install(self, spec, prefix):
-        make()
-        if self.run_tests:
-            make('test')
         make('install', 'PREFIX={0}'.format(prefix))