diff options
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) |