From cdeecf2507d92c41625c9d7d3ee21b973c404f5b Mon Sep 17 00:00:00 2001
From: dunatotatos <contact@dunatotatos.com>
Date: Fri, 16 Oct 2020 10:17:32 +0200
Subject: GenomeWorks: added new package at v0.5.3 (#19263)

---
 .../builtin/packages/genomeworks/3rdparty.patch    | 11 +++++
 .../repos/builtin/packages/genomeworks/package.py  | 48 ++++++++++++++++++++++
 2 files changed, 59 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/genomeworks/3rdparty.patch
 create mode 100644 var/spack/repos/builtin/packages/genomeworks/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/genomeworks/3rdparty.patch b/var/spack/repos/builtin/packages/genomeworks/3rdparty.patch
new file mode 100644
index 0000000000..34930a25ee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/genomeworks/3rdparty.patch
@@ -0,0 +1,11 @@
+--- a/cmake/3rdparty.cmake	2020-10-08 19:23:46.717478760 +0200
++++ b/cmake/3rdparty.cmake	2020-10-08 19:26:29.251160827 +0200
+@@ -46,7 +46,7 @@
+ add_library(cub INTERFACE IMPORTED)
+ #target_include_directories(cub INTERFACE ${CUB_DIR}>) does not work with
+ #cmake before 3.11, use the following for now:
+-set_property(TARGET cub APPEND PROPERTY INTERFACE_INCLUDE_DIRECTORIES "${CUB_DIR}")
+-#set_property(TARGET cub APPEND PROPERTY INTERFACE_INCLUDE_DIRECTORIES "${CUB_DIR}")
+ 
+ set(KSEQPP_DIR ${PROJECT_SOURCE_DIR}/3rdparty/kseqpp/src CACHE STRING
+     "Path to kseqpp repo")
diff --git a/var/spack/repos/builtin/packages/genomeworks/package.py b/var/spack/repos/builtin/packages/genomeworks/package.py
new file mode 100644
index 0000000000..fce2e91d81
--- /dev/null
+++ b/var/spack/repos/builtin/packages/genomeworks/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2020 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 Genomeworks(CMakePackage, CudaPackage):
+    """SDK for GPU accelerated genome assembly and analysis."""
+
+    homepage = "https://clara-parabricks.github.io/GenomeWorks/"
+    url      = "https://github.com/clara-parabricks/GenomeWorks/archive/v0.5.3.tar.gz"
+    git      = "https://github.com/clara-parabricks/GenomeWorks.git"
+
+    version('0.5.3', tag='v0.5.3', submodules=True)
+    version('0.5.2', tag='v0.5.2', submodules=True)
+    version('0.5.1', tag='v0.5.1', submodules=True)
+    version('0.5.0', tag='v0.5.0', submodules=True)
+    version('0.4.4', tag='v0.4.4', submodules=True)
+    version('0.4.3', tag='v0.4.3', submodules=True)
+    version('0.4.0', tag='v0.4.0', submodules=True)
+    version('0.3.0', tag='v0.3.0', submodules=True)
+    version('0.2.0', tag='v0.2.0', submodules=True)
+
+    depends_on('cmake@3.10.2:', type=('build'))
+    depends_on('cuda@11:', type=('build', 'run'))
+    depends_on('python@3.6.7:', type=('build', 'run'))
+
+    # Disable CUB compilation, as it is already included in CUDA 11.
+    # See https://github.com/clara-parabricks/GenomeWorks/issues/570
+    # This patch breaks GenomeWorks with Cuda <11, cuda@11: is
+    # therefore used as dependency.
+    patch('3rdparty.patch')
+
+    def cmake_args(self):
+        args = []
+        spec = self.spec
+        if '+cuda' in spec:
+            args.append('-DWITH_CUDA=ON')
+            args.append('-Dgw_cuda_gen_all_arch=ON')
+            args.append('-DTHRUST_IGNORE_CUB_VERSION_CHECK=ON')
+            cuda_arch = spec.variants['cuda_arch'].value
+            if cuda_arch != 'none':
+                args.append('-DCUDA_FLAGS=-arch=sm_{0}'.format(cuda_arch[0]))
+        else:
+            args.append('-DWITH_CUDA=OFF')
+        return args
-- 
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