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-rw-r--r--var/spack/repos/builtin/packages/fasta/package.py77
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+##############################################################################
+# 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')