diff options
Diffstat (limited to 'var')
-rw-r--r-- | var/spack/repos/builtin/packages/fasta/package.py | 77 |
1 files changed, 77 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/fasta/package.py b/var/spack/repos/builtin/packages/fasta/package.py new file mode 100644 index 0000000000..55e30ece73 --- /dev/null +++ b/var/spack/repos/builtin/packages/fasta/package.py @@ -0,0 +1,77 @@ +############################################################################## +# 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 +############################################################################## +from spack import * + + +class Fasta(MakefilePackage): + """The FASTA programs find regions of local or global similarity + between Protein or DNA sequences, either by searching Protein or + DNA databases, or by identifying local duplications within a + sequence. Other programs provide information on the statistical + significance of an alignment. Like BLAST, FASTA can be used to + infer functional and evolutionary relationships between sequences + as well as help identify members of gene families. + """ + + homepage = "https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml" + url = "https://github.com/wrpearson/fasta36/archive/fasta-v36.3.8g.tar.gz" + + version('36.3.8g', sha256='fa5318b6f8d6a3cfdef0d29de530eb005bfd3ca05835faa6ad63663f8dce7b2e') + + depends_on('zlib') + + # The src tree includes a plethora of variant Makefiles and the + # builder is expected to choose one that's appropriate. This'll + # do for a first cut. I can't test anything else.... + @property + def makefile_name(self): + if self.spec.satisfies('platform=darwin'): + name = 'Makefile.os_x86_64' + elif (self.spec.satisfies('platform=linux') and + self.spec.satisfies('target=x86_64')): + name = 'Makefile.linux64_sse2' + else: + tty.die('''Unsupported platform/target, must be +Darwin (assumes 64-bit) +Linux x86_64 +''') + return name + + @property + def makefile_path(self): + return join_path(self.stage.source_path, 'make', self.makefile_name) + + def edit(self, spec, prefix): + makefile = FileFilter(self.makefile_path) + makefile.filter('XDIR = .*', 'XDIR = {0}'.format(prefix.bin)) + + def build(self, spec, prefix): + with working_dir('src'): + make('-f', self.makefile_path) + + def install(self, spec, prefix): + with working_dir('src'): + mkdir(prefix.bin) + make('-f', self.makefile_path, 'install') |