gcta: rework package recipe (#30286)

2 files changed, 85 insertions, 10 deletions

diff --git a/var/spack/repos/builtin/packages/gcta/package.py b/var/spack/repos/builtin/packages/gcta/package.py
index 8136742a04..76cbfc265b 100644
--- a/var/spack/repos/builtin/packages/gcta/package.py
+++ b/var/spack/repos/builtin/packages/gcta/package.py
@@ -6,24 +6,69 @@
 from spack import *
 
 
-class Gcta(Package):
-
+class Gcta(CMakePackage):
     """GCTA (Genome-wide Complex Trait Analysis) was originally designed to
     estimate the proportion of phenotypic variance explained by all genome-wide
     SNPs for complex traits (the GREML method), and has subsequently extended
     for many other analyses to better understand the genetic architecture of
     complex traits. GCTA currently supports the following analyses."""
 
-    homepage = "https://cnsgenomics.com/software/gcta/#Overview"
-    url      = "http://cnsgenomics.com/software/gcta/gcta_1.91.2beta.zip"
+    homepage = "https://github.com/jianyangqt/gcta"
+    url      = "https://github.com/jianyangqt/gcta/archive/refs/tags/v1.91.2.tar.gz"
+    git      = "https://github.com/jianyangqt/gcta.git"
+    maintainers = ['snehring']
+
+    version('1.94.0beta',  commit='746e3975ddb463fc7bd15b03c6cc64b023eca497', submodules=True)
+    version('1.91.2',      sha256='0609d0fba856599a2acc66adefe87725304117acc226360ec2aabf8a0ac64e85')
+
+    conflicts('target=aarch64:', when='@:1.91.2', msg='aarch64 support added in 1.94.0')
+
+    depends_on('cmake@3.1:', type='build')
+    depends_on('intel-mkl@2017:', when='target=x86_64:')
+    depends_on('openblas', when='target=aarch64:')
+    depends_on('eigen@3.3.1', when='@1.91.2')
+    depends_on('eigen@3.3.7:', when='@1.94.0beta:')
+    depends_on('boost@1.79:', when='@1.94.0beta:')
+    depends_on('zlib')
+    depends_on('sqlite@3.3.1:', when='@1.94.0beta:')
+    depends_on('zstd@1.4.4:', when='@1.94.0beta:')
+    depends_on('spectra', when='@1.94.0beta:')
+    depends_on('gsl', when='@1.94.0beta:')
+
+    def patch(self):
+        # allow us to specify the locations with cmake_args
+        strings = [
+            'SET(EIGEN3_INCLUDE_DIR "$ENV{EIGEN3_INCLUDE_DIR}")',
+            'SET(SPECTRA_LIB "$ENV{SPECTRA_LIB}")',
+            'SET(BOOST_LIB "$ENV{BOOST_LIB}")',
+            'SET(OPENBLAS "$ENV{OPENBLAS}")',
+            'SET(MKLROOT "$ENV{MKLROOT}")'
+        ]
+        for s in strings:
+            filter_file(s, '', 'CMakeLists.txt', string=True)
+
+    def cmake_args(self):
+        eigen = self.spec['eigen'].prefix.include
+        args = [self.define('EIGEN3_INCLUDE_DIR', eigen)]
+        if self.spec.satisfies('@1.94.0beta:'):
+            spectra = self.spec['spectra'].prefix.include
+            boost = self.spec['boost'].prefix.include
+            deps = [
+                self.define('SPECTRA_LIB', spectra),
+                self.define('BOOST_LIB', boost),
+            ]
+            args.extend(deps)
 
-    version('1.91.2beta_mac', 'ce0882ad35dd9474ffe40911da369274700af1ecb9916c0a355b7bad14850234')
-    version('1.91.2beta', '192efb767be1c7ca9c2dac5d2c2317a97c7a9db1f801168d19ad2a51b98d9b10', preferred=True)
+        if self.spec.satisfies('target=x86_64:'):
+            mkl = self.spec['intel-mkl'].prefix
+            args.append(self.define('MKLROOT', mkl))
+        elif self.spec.satisfies('target=aarch64:'):
+            openblas = self.spec['openblas'].prefix
+            args.append(self.define('OPENBLAS', openblas))
 
-    conflicts('@1.91.2beta', when='platform=darwin')
-    conflicts('@1.91.2beta_mac', when='platform=linux')
+        return args
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
-        install('gcta64', join_path(prefix.bin, 'gcta64'))
-        set_executable(join_path(prefix.bin, 'gcta64'))
+        with working_dir(self.build_directory):
+            install('gcta64', join_path(prefix.bin, 'gcta64'))
diff --git a/var/spack/repos/builtin/packages/spectra/package.py b/var/spack/repos/builtin/packages/spectra/package.py
new file mode 100644
index 0000000000..14a3e8ba6b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/spectra/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Spectra(CMakePackage):
+    """
+    Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned
+    ARPACK. It is a C++ library for large scale eigenvalue problems,
+    built on top of Eigen, an open source linear algebra library.
+
+    Spectra is implemented as a header-only C++ library, whose only
+    dependency, Eigen, is also header-only. Hence Spectra can be easily
+    embedded in C++ projects that require calculating eigenvalues of
+    large matrices.
+    """
+
+    homepage = "https://spectralib.org/"
+    url      = "https://github.com/yixuan/spectra/archive/refs/tags/v1.0.1.tar.gz"
+    maintainers = ['snehring']
+
+    version('1.0.1', sha256='919e3fbc8c539a321fd5a0766966922b7637cc52eb50a969241a997c733789f3')
+    version('1.0.0', sha256='45228b7d77b916b5384245eb13aa24bc994f3b0375013a8ba6b85adfd2dafd67')
+    version('0.9.0', sha256='2966757d432e8fba5958c2a05ad5674ce34eaae3718dd546c1ba8760b80b7a3d')
+
+    depends_on('cmake@3.5:')
+    depends_on('eigen')