libbeagle package: add cuda support (#10650)

libbeagle compiles against CUDA by default but no there is no mention
of it in the package recipe. This PR adds explicit cuda paths and
variants, and fixes the target architecture as well (for those who
don't have compute_13)

var/spack/repos/builtin/packages/libbeagle/package.py

@@ -6,7 +6,7 @@
 from spack import *
 
 
-class Libbeagle(AutotoolsPackage):
+class Libbeagle(AutotoolsPackage, CudaPackage):
     """Beagle performs genotype calling, genotype phasing, imputation of
        ungenotyped markers, and identity-by-descent segment detection."""
 
@@ -24,6 +24,33 @@ class Libbeagle(AutotoolsPackage):
     depends_on('pkgconfig', type='build')
     depends_on('java', type='build')
 
+    def patch(self):
+        # update cuda architecture if necessary
+        if '+cuda' in self.spec:
+            arch = self.spec.variants['cuda_arch'].value
+            archflag = ''
+
+            if arch[0] != 'none':
+                archflag = '-arch=%s' % arch[0]
+
+            filter_file('-arch compute_13', archflag,
+                        'libhmsbeagle/GPU/kernels/Makefile.am',
+                        string=True)
+
+            # point CUDA_LIBS to libcuda.so
+            filter_file('-L$with_cuda/lib', '-L$with_cuda/lib64/stubs',
+                        'configure.ac', string=True)
+
+    def configure_args(self):
+        args = []
+
+        if '+cuda' in self.spec:
+            args.append('--with-cuda=%s' % spec['cuda'].prefix)
+        else:
+            args.append('--without-cuda')
+
+        return args
+
     def url_for_version(self, version):
         url = "https://github.com/beagle-dev/beagle-lib/archive/beagle_release_{0}.tar.gz"
         return url.format(version.underscored)