diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/blast-plus/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/blast-plus/package.py | 212 |
1 files changed, 88 insertions, 124 deletions
diff --git a/var/spack/repos/builtin/packages/blast-plus/package.py b/var/spack/repos/builtin/packages/blast-plus/package.py index e886d0ac3b..9faef127ed 100644 --- a/var/spack/repos/builtin/packages/blast-plus/package.py +++ b/var/spack/repos/builtin/packages/blast-plus/package.py @@ -10,17 +10,17 @@ class BlastPlus(AutotoolsPackage): """Basic Local Alignment Search Tool.""" homepage = "https://blast.ncbi.nlm.nih.gov/" - url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-src.tar.gz" + url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-src.tar.gz" - maintainers = ['weijianwen'] + maintainers = ["weijianwen"] - version('2.12.0', sha256='fda3c9c9d488cad6c1880a98a236d842bcf3610e3e702af61f7a48cf0a714b88') - version('2.11.0', sha256='d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954') - version('2.9.0', sha256='a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257') - version('2.8.1', sha256='e03dd1a30e37cb8a859d3788a452c5d70ee1f9102d1ee0f93b2fbd145925118f') - version('2.7.1', sha256='10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca') - version('2.6.0', sha256='0510e1d607d0fb4389eca50d434d5a0be787423b6850b3a4f315abc2ef19c996') - version('2.2.30', sha256='26f72d51c81b9497f33b7274109565c36692572faef4d72377f79b7e59910e40') + version("2.12.0", sha256="fda3c9c9d488cad6c1880a98a236d842bcf3610e3e702af61f7a48cf0a714b88") + version("2.11.0", sha256="d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954") + version("2.9.0", sha256="a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257") + version("2.8.1", sha256="e03dd1a30e37cb8a859d3788a452c5d70ee1f9102d1ee0f93b2fbd145925118f") + version("2.7.1", sha256="10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca") + version("2.6.0", sha256="0510e1d607d0fb4389eca50d434d5a0be787423b6850b3a4f315abc2ef19c996") + version("2.2.30", sha256="26f72d51c81b9497f33b7274109565c36692572faef4d72377f79b7e59910e40") # homebrew sez: Fixed upstream in future version > 2.6 # But this bug sez that it will be fixed in 2.6 @@ -30,110 +30,90 @@ class BlastPlus(AutotoolsPackage): # 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") + 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') + @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) + 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("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') - variant('perl', default=True, - description='Build with perl support') - variant('python', default=True, - description='Build with python support') - - depends_on('jpeg', when='+jpeg') - depends_on('libpng', when='+png') - depends_on('freetype', when='+freetype') + 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") + variant("perl", default=True, description="Build with perl support") + variant("python", default=True, description="Build with python 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("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', when='+python') - depends_on('perl', when='+perl') + depends_on("python", when="+python") + depends_on("perl", when="+perl") - depends_on('lmdb', when='@2.7.1:') + depends_on("lmdb", when="@2.7.1:") - configure_directory = 'c++' + configure_directory = "c++" def configure_args(self): - spec = self.spec + spec = self.spec config_args = [ - '--with-bin-release', - '--without-debug', - '--with-mt', - '--without-boost', + "--with-bin-release", + "--without-debug", + "--with-mt", + "--without-boost", ] - if spec.target.family != 'aarch64': - config_args.append('--with-64') - if '+static' in spec: - config_args.append('--with-static') + if spec.target.family != "aarch64": + config_args.append("--with-64") + 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) - ) + 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') + config_args.append("--without-jpeg") - if '+png' in spec: - config_args.append( - '--with-png={0}'.format(self.spec['libpng'].prefix) - ) + if "+png" in spec: + config_args.append("--with-png={0}".format(self.spec["libpng"].prefix)) else: - config_args.append('--without-png') + config_args.append("--without-png") - if '+freetype' in spec: - config_args.append( - '--with-freetype={0}'.format(self.spec['freetype'].prefix) - ) + 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-freetype") - config_args.append('--without-hdf5') + config_args.append("--without-hdf5") # if '+hdf5' in spec: # # FIXME # config_args.append( @@ -142,60 +122,44 @@ class BlastPlus(AutotoolsPackage): # else: # config_args.append('--without-hdf5') - if '+zlib' in spec: - config_args.append( - '--with-z={0}'.format(self.spec['zlib'].prefix) - ) + if "+zlib" in spec: + config_args.append("--with-z={0}".format(self.spec["zlib"].prefix)) else: - config_args.append('--without-z') + config_args.append("--without-z") - if '+bzip2' in spec: - config_args.append( - '--with-bz2={0}'.format(self.spec['bzip2'].prefix) - ) + if "+bzip2" in spec: + config_args.append("--with-bz2={0}".format(self.spec["bzip2"].prefix)) else: - config_args.append('--without-bz2') + config_args.append("--without-bz2") - if '+lzo' in spec: - config_args.append( - '--with-lzo={0}'.format(self.spec['lzo'].prefix) - ) + if "+lzo" in spec: + config_args.append("--with-lzo={0}".format(self.spec["lzo"].prefix)) else: - config_args.append('--without-lzo') + config_args.append("--without-lzo") - if '+gnutls' in spec: - config_args.append( - '--with-gnutls={0}'.format(self.spec['gnutls'].prefix) - ) + if "+gnutls" in spec: + config_args.append("--with-gnutls={0}".format(self.spec["gnutls"].prefix)) else: - config_args.append('--without-gnutls') + config_args.append("--without-gnutls") - if '+openssl' in spec: - config_args.append( - '--with-openssl={0}'.format(self.spec['openssl'].prefix) - ) + if "+openssl" in spec: + config_args.append("--with-openssl={0}".format(self.spec["openssl"].prefix)) else: - config_args.append('--without-openssl') + config_args.append("--without-openssl") - if '+pcre' in spec: - config_args.append( - '--with-pcre={0}'.format(self.spec['pcre'].prefix) - ) + if "+pcre" in spec: + config_args.append("--with-pcre={0}".format(self.spec["pcre"].prefix)) else: - config_args.append('--without-pcre') + config_args.append("--without-pcre") - if '+python' in spec: - config_args.append( - '--with-python={0}'.format(self.spec['python'].home) - ) + if "+python" in spec: + config_args.append("--with-python={0}".format(self.spec["python"].home)) else: - config_args.append('--without-python') + config_args.append("--without-python") - if '+perl' in spec: - config_args.append( - '--with-perl={0}'.format(self.spec['perl'].prefix) - ) + if "+perl" in spec: + config_args.append("--with-perl={0}".format(self.spec["perl"].prefix)) else: - config_args.append('--without-python') + config_args.append("--without-python") return config_args |