Merge remote-tracking branch 'upstream/develop' into krell_spack_updates

Conflicts: var/spack/repos/builtin/packages/openspeedshop/package.py
2017-07-27 09:29:40 -05:00 · 2017-07-27 09:29:40 -05:00 · 3c914d888a
commit 3c914d888a
parent a1274a7f51 ddc1dcd084
80 changed files with 926 additions and 388 deletions
--- 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:

--- 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:
--- 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),
--- 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)
--- 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):
--- 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',
--- 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))
--- 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',
--- 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.',
--- 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'
--- 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),
--- 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")
--- 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"
--- 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

--- 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
--- 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
--- 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',
--- 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 = []
--- a/var/spack/repos/builtin/packages/cleaveland4/package.py
+++ 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)
--- 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 = []
--- 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 = []
--- 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')
--- 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'
--- 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

--- 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']

--- 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(
--- 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'
--- 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']

--- 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

--- 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')

--- 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
--- 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=' +
--- 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'
--- 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)
--- 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
--- 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',
--- 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

--- 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):
        """
--- 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'
--- 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')
--- 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 = []
--- 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')
--- 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')
--- 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):
--- 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"
--- 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'
--- a/var/spack/repos/builtin/packages/perl-math-cdf/package.py
+++ 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')
--- 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']

--- 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) + '/'
--- 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'
--- 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')
--- 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',
--- 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
--- a/var/spack/repos/builtin/packages/shortstack/package.py
+++ 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)
--- a/var/spack/repos/builtin/packages/snptest/package.py
+++ 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)
--- a/var/spack/repos/builtin/packages/stacks/package.py
+++ 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
--- a/var/spack/repos/builtin/packages/stringtie/package.py
+++ 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)
--- a/var/spack/repos/builtin/packages/structure/package.py
+++ 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)
--- 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)
--- a/var/spack/repos/builtin/packages/subread/package.py
+++ 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)
--- a/var/spack/repos/builtin/packages/sumaclust/package.py
+++ 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)
--- a/var/spack/repos/builtin/packages/swarm/package.py
+++ 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)
--- 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'),
--- a/var/spack/repos/builtin/packages/tabix/package.py
+++ 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)
--- 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']
--- a/var/spack/repos/builtin/packages/transdecoder/package.py
+++ 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)
--- a/var/spack/repos/builtin/packages/transposome/package.py
+++ 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')
--- 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'),

--- a/var/spack/repos/builtin/packages/trimgalore/package.py
+++ 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)
--- 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'))
--- 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',
--- a/var/spack/repos/builtin/packages/viennarna/package.py
+++ 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
--- 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'
--- 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'
--- 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'
--- 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'
--- 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'
--- 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']

--- 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',
--- 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))