hapdip: Create new package and its dependency k8. (#7685)

* k8: Create new package.

* hapdip: Create new package.

* Change description.

2 files changed, 85 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/hapdip/package.py b/var/spack/repos/builtin/packages/hapdip/package.py
new file mode 100644
index 0000000000..066282c461
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hapdip/package.py
@@ -0,0 +1,39 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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/spack/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 Hapdip(Package):
+    """The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from
+    WGS Illumina data."""
+
+    homepage = "https://github.com/lh3/hapdip"
+
+    version('2018.02.20', git='https://github.com/lh3/hapdip.git', commit='7c12f684471999a543fdacce972c9c86349758a3')
+
+    depends_on('k8', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/k8/package.py b/var/spack/repos/builtin/packages/k8/package.py
new file mode 100644
index 0000000000..801323229d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/k8/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/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
+##############################################################################
+import sys
+import os
+from spack import *
+
+
+class K8(Package):
+    """K8 is a Javascript shell based on Google's V8 Javascript engine."""
+
+    homepage = "https://github.com/attractivechaos/k8"
+    url      = "https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2"
+
+    version('0.2.4', 'edc5579ff18842a2a59aa92ce8bab8b4')
+
+    depends_on('zlib', type='run')
+
+    def install(self, spec, prefix):
+        if (sys.platform == 'darwin'):
+            os.rename('k8-Darwin', 'k8')
+
+        if (sys.platform != 'darwin'):
+            os.rename('k8-Linux', 'k8')
+        install_tree('.', prefix.bin)