tcoffee: new package (#5185)

4 files changed, 142 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/dialign-tx/package.py b/var/spack/repos/builtin/packages/dialign-tx/package.py
index ccb094605e..29a0c800da 100644
--- a/var/spack/repos/builtin/packages/dialign-tx/package.py
+++ b/var/spack/repos/builtin/packages/dialign-tx/package.py
@@ -48,3 +48,5 @@ class DialignTx(MakefilePackage):
         mkdirp(prefix.bin)
         with working_dir(self.build_directory):
             install('dialign-tx', prefix.bin)
+            # t-coffee recognizes as dialign-t
+            install('dialign-tx', join_path(prefix.bin, 'dialign-t'))
diff --git a/var/spack/repos/builtin/packages/probconsrna/package.py b/var/spack/repos/builtin/packages/probconsrna/package.py
new file mode 100644
index 0000000000..4973ced565
--- /dev/null
+++ b/var/spack/repos/builtin/packages/probconsrna/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# 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 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 Probconsrna(Package):
+    """Experimental version of PROBCONS with parameters estimated via
+       unsupervised training on BRAliBASE """
+
+    homepage = "http://probcons.stanford.edu/"
+    url      = "http://probcons.stanford.edu/probconsRNA.tar.gz"
+
+    version('2005-6-7', '2aa13012124208ca5dd6b0a1d508208d')
+
+    def install(self, build, prefix):
+        mkdirp(prefix.bin)
+        install('compare', prefix.bin)
+        install('makegnuplot', prefix.bin)
+        install('probcons', prefix.bin)
+        # needed for tcoffee
+        install('probcons', prefix.bin.probconsRNA)
+        install('project', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/tcoffee/package.py b/var/spack/repos/builtin/packages/tcoffee/package.py
new file mode 100644
index 0000000000..0f954b42c7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tcoffee/package.py
@@ -0,0 +1,57 @@
+##############################################################################
+# 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 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 Tcoffee(MakefilePackage):
+    """T-Coffee is a multiple sequence alignment program."""
+
+    homepage = "http://www.tcoffee.org/"
+    url      = "https://github.com/cbcrg/tcoffee"
+
+    version('2017-08-17', git='https://github.com/cbcrg/tcoffee.git', commit='f389b558e91d0f82e7db934d9a79ce285f853a71')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('blast-plus')
+    depends_on('dialign-tx')
+    depends_on('viennarna')
+    depends_on('clustalw')
+    depends_on('tmalign')
+    depends_on('muscle')
+    depends_on('mafft')
+    depends_on('pcma')
+    depends_on('poamsa')
+    depends_on('probconsrna')
+
+    build_directory = 'compile'
+
+    def build(self, spec, prefix):
+        with working_dir(self.build_directory):
+            make('t_coffee')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        with working_dir(self.build_directory):
+            install('t_coffee', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/tmalign/package.py b/var/spack/repos/builtin/packages/tmalign/package.py
new file mode 100644
index 0000000000..5f08bb27fc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tmalign/package.py
@@ -0,0 +1,39 @@
+##############################################################################
+# 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 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 Tmalign(Package):
+    """TM-align is an algorithm for sequence-order independent protein
+       structure comparisons."""
+
+    homepage = "http://zhanglab.ccmb.med.umich.edu/TM-align"
+    url      = "http://zhanglab.ccmb.med.umich.edu/TM-align/TM-align-C/TMalignc.tar.gz"
+
+    version('2016-05-25', 'c1027e4b65c07d1c5df9717de7417118')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('TMalign', prefix.bin)