diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/blast-plus/blast-make-fix2.5.0.diff | 22 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/blast-plus/package.py | 207 |
2 files changed, 229 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/blast-plus/blast-make-fix2.5.0.diff b/var/spack/repos/builtin/packages/blast-plus/blast-make-fix2.5.0.diff new file mode 100644 index 0000000000..5611a0e83b --- /dev/null +++ b/var/spack/repos/builtin/packages/blast-plus/blast-make-fix2.5.0.diff @@ -0,0 +1,22 @@ +--- ncbi-blast-2.5.0+-src/c++/src/build-system/Makefile.in.top 2014-11-12 17:41:55.000000000 +0100 ++++ MakeFile 2016-12-19 18:00:58.000000000 +0100 +@@ -1,4 +1,4 @@ +-# $Id: Makefile.in.top 451817 2014-11-12 16:41:55Z ucko $ ++# $Id$ + # Top-level meta-makefile that simplifies building even further. + + # include @builddir@/Makefile.mk +@@ -49,9 +49,10 @@ + for x in *.a; do \ + $(LN_S) "$$x" "`$(BASENAME) \"$$x\" .a`-static.a"; \ + done +- cd $(includedir0) && find * -name CVS -prune -o -print |\ +- cpio -pd $(pincludedir) +- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) ++ #for d in $(includedir0) $(incdir); do \ ++ # cd $$d && find * -name .svn prune -o -print | \ ++ # cpio -pd $(pincludedir) ; \ ++ #done + ## set up appropriate build and status directories somewhere under $(libdir)? + + install-gbench: diff --git a/var/spack/repos/builtin/packages/blast-plus/package.py b/var/spack/repos/builtin/packages/blast-plus/package.py new file mode 100644 index 0000000000..02db14f478 --- /dev/null +++ b/var/spack/repos/builtin/packages/blast-plus/package.py @@ -0,0 +1,207 @@ +############################################################################## +# 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 +############################################################################## +# +# This is a based largely on the Homebrew science formula: +# https://github.com/Homebrew/homebrew-science/blob/master/blast.rb +# +# There s one tricky bit to be resolved: +# +# - HDF5 builds explode, blast's configure script tries to run a program that +# uses a variable called 'HOST' but some other bit defines a macro called +# HOST that's defined to a string. Hilarity ensues. +# +# +from spack import * + + +class BlastPlus(AutotoolsPackage): + """Basic Local Alignment Search Tool.""" + + + homepage = "http://blast.ncbi.nlm.nih.gov/" + url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz" + + def url_for_version(self, version): + url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/{0}/ncbi-blast-{0}+-src.tar.gz" + return url.format(version) + + version('2.6.0', 'c8ce8055b10c4d774d995f88c7cc6225') + version('2.2.30', 'f8e9a5eb368173142fe6867208b73715') + + # homebrew sez: Fixed upstream in future version > 2.6 + # But this bug sez that it will be fixed in 2.6 + # https://github.com/Homebrew/homebrew-science/pull/4740 + # The 2.6.0 src still matches the "before" bit of the patch + # so it's probably still "needed". + # On the other hand, the `find` command is broken and there + # aren't any .svn dirs in the tree, so I've updated their patch + # to just comment out the block. + patch('blast-make-fix2.5.0.diff', when="@2.5.0:2.6.0") + + # See https://github.com/Homebrew/homebrew-science/issues/2337#issuecomment-170011511 + @when('@:2.2.31') + def patch(self): + filter_file("2.95* | 2.96* | 3.* | 4.* )", + "2.95* | 2.96* | 3.* | 4.* | 5.* )", + "c++/src/build-system/configure", + string=True) + + # No... + # depends_on :mysql => :optional + + variant('static', default=False, + description='Build with static linkage') + variant('jpeg', default=True, + description='Build with jpeg support') + variant('png', default=True, + description='Build with png support') + variant('freetype', default=True, + description='Build with freetype support') + # variant('hdf5', default=True, + # description='Build with hdf5 support') + variant('gnutls', default=True, + description='Build with gnutls support') + variant('openssl', default=True, + description='Build with openssl support') + variant('zlib', default=True, + description='Build with zlib support') + variant('bzip2', default=True, + description='Build with bzip2 support') + variant('lzo', default=True, + description='Build with lzo support') + variant('pcre', default=True, + description='Build with pcre support') + + depends_on('jpeg', when='+jpeg') + depends_on('libpng', when='+png') + depends_on('freetype', when='+freetype') + # depends_on('hdf5', when='+hdf5') + depends_on('gnutls', when='+gnutls') + depends_on('openssl', when='+openssl') + depends_on('zlib', when='+zlib') + depends_on('bzip2', when='+bzip2') + depends_on('lzo', when='+lzo') + depends_on('pcre', when='+pcre') + + depends_on('python') + + configure_directory = 'c++' + + def configure_args(self): + spec = self.spec + + config_args = [ + '--with-bin-release', + '--without-debug', + '--with-mt', + '--with-64', + '--without-boost', + ] + + if '+static' in spec: + config_args.append('--with-static') + # FIXME + # args << "--with-static-exe" unless OS.linux? + # args << "--with-dll" if build.with? "dll" + else: + config_args.extend([ + '--with-dll', + '--without-static', + '--without-static-exe' + ]) + + if '+jpeg' in spec: + config_args.append( + '--with-jpeg={0}'.format(self.spec['jpeg'].prefix) + ) + else: + config_args.append('--without-jpeg') + + if '+png' in spec: + config_args.append( + '--with-png={0}'.format(self.spec['libpng'].prefix) + ) + else: + config_args.append('--without-png') + + if '+freetype' in spec: + config_args.append( + '--with-freetype={0}'.format(self.spec['freetype'].prefix) + ) + else: + config_args.append('--without-freetype') + + config_args.append('--without-hdf5') + # if '+hdf5' in spec: + # # FIXME + # config_args.append( + # '--with-hdf5={0}'.format(self.spec['hdf5'].prefix) + # ) + # else: + # config_args.append('--without-hdf5') + + if '+zlib' in spec: + config_args.append( + '--with-z={0}'.format(self.spec['zlib'].prefix) + ) + else: + config_args.append('--without-z') + + if '+bzip2' in spec: + config_args.append( + '--with-bz2={0}'.format(self.spec['bzip2'].prefix) + ) + else: + config_args.append('--without-bz2') + + if '+lzo' in spec: + config_args.append( + '--with-lzo={0}'.format(self.spec['lzo'].prefix) + ) + else: + config_args.append('--without-lzo') + + if '+gnutls' in spec: + config_args.append( + '--with-gnutls={0}'.format(self.spec['gnutls'].prefix) + ) + else: + config_args.append('--without-gnutls') + + if '+openssl' in spec: + config_args.append( + '--with-openssl={0}'.format(self.spec['openssl'].prefix) + ) + else: + config_args.append('--without-openssl') + + if '+pcre' in spec: + config_args.append( + '--with-pcre={0}'.format(self.spec['pcre'].prefix) + ) + else: + config_args.append('--without-pcre') + + return config_args |