minimap2: new package (#5722)

2 files changed, 77 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/minimap2/package.py b/var/spack/repos/builtin/packages/minimap2/package.py
new file mode 100644
index 0000000000..74835b7950
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minimap2/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# 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/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 Minimap2(MakefilePackage):
+    """Minimap2 is a versatile sequence alignment program that aligns DNA or
+       mRNA sequences against a large reference database."""
+
+    homepage = "https://github.com/lh3/minimap2"
+    url      = "https://github.com/lh3/minimap2/releases/download/v2.2/minimap2-2.2.tar.bz2"
+
+    version('2.2', '5b68e094f4fa3dfbd9b37d5b654b7715')
+
+    depends_on('py-mappy', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('minimap2', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/py-mappy/package.py b/var/spack/repos/builtin/packages/py-mappy/package.py
new file mode 100644
index 0000000000..80dddd10b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-mappy/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# 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/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 PyMappy(PythonPackage):
+    """Mappy provides a convenient interface to minimap2."""
+
+    homepage = "https://pypi.python.org/pypi/mappy"
+    url      = "https://pypi.io/packages/source/m/mappy/mappy-2.2.tar.gz"
+
+    version('2.2', 'dfc2aefe98376124beb81ce7dcefeccb')
+
+    depends_on('zlib')