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authorGeorge Hartzell <hartzell@alerce.com>2017-06-01 10:36:01 -0700
committerAdam J. Stewart <ajstewart426@gmail.com>2017-06-01 12:36:01 -0500
commit391afa9271f90424917262c48b91b2d9c2a00e2f (patch)
treed7533bb07ee6459290dad99eceac721f3f30c855 /var
parent916243b23a534ce78d9fde6ad0c52b740a9d84e0 (diff)
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Add packages for clustalw and clustalo (and argtable) (#4412)
* Add packages for clustalw and clustalo (and argtable) Add packages for the classic multiple alignment package, `clustalw` and its younger sibling, `clustalo`. `clustalo` needed the `argtable` package (command line arg parsing). Lightly tested on CentOS 7. * Remove FIXME (sigh...)
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/argtable/package.py36
-rw-r--r--var/spack/repos/builtin/packages/clustalo/package.py36
-rw-r--r--var/spack/repos/builtin/packages/clustalw/package.py34
3 files changed, 106 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/argtable/package.py b/var/spack/repos/builtin/packages/argtable/package.py
new file mode 100644
index 0000000000..8e1bec15f9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/argtable/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 Argtable(AutotoolsPackage):
+ """Argtable is an ANSI C library for parsing GNU style command line
+ options with a minimum of fuss.
+ """
+
+ homepage = "http://argtable.sourceforge.net/"
+ url = "https://sourceforge.net/projects/argtable/files/argtable/argtable-2.13/argtable2-13.tar.gz/download"
+
+ version('2-13', '156773989d0d6406cea36526d3926668')
diff --git a/var/spack/repos/builtin/packages/clustalo/package.py b/var/spack/repos/builtin/packages/clustalo/package.py
new file mode 100644
index 0000000000..9e985f0cd7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/clustalo/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 Clustalo(AutotoolsPackage):
+ """Clustal Omega: the last alignment program you'll ever need."""
+
+ homepage = "http://www.clustal.org/omega/"
+ url = "http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz"
+
+ version('1.2.4', '6c0459f4c463a30e942ce7e0efc91422')
+
+ depends_on('argtable')
diff --git a/var/spack/repos/builtin/packages/clustalw/package.py b/var/spack/repos/builtin/packages/clustalw/package.py
new file mode 100644
index 0000000000..97f193c628
--- /dev/null
+++ b/var/spack/repos/builtin/packages/clustalw/package.py
@@ -0,0 +1,34 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 LICENSE file 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 Clustalw(AutotoolsPackage):
+ """Multiple alignment of nucleic acid and protein sequences."""
+
+ homepage = "http://www.clustal.org/clustal2/"
+ url = "http://www.clustal.org/download/2.1/clustalw-2.1.tar.gz"
+
+ version('2.1', '144df8440a0ae083d5167616c8ceeb41')