Add Blast+ package. (#3562)

* Add Blast+ package.

Adds support for NCBI's blast+@2.6.0.  I'll be adding a few historical versions in the near future.

It's a fairly direct transliteration of the [Homebrew Science recipe][hbs].

I skipped the mysql support.

There is a problem with HDF5 support.  Blast's configure script test program defines a macro 'HOST' to a string value and one of the HDF5 bits has an variable named 'HOST'.  Fun things happen.   I've disabled support for now.

I've run very very basic tests.  I'll get this out to my users and ensure that it works and fine tune the options and etc....

[hbs]: https://github.com/Homebrew/homebrew-science/blob/master/blast.rb

* Flake8 fixes

* Update w.t.r. mamelara's PR and cleanup

Add paths to things in the --with-* config args

Add add'l config flags from #3394.

Update patch to no-op and add comment.

Add add'l dependencies after studying `configure --help`.

* Flake8 cleanup

* Add support for blast+@2.2.30

Need to work around a configure bug.  See https://github.com/Homebrew/homebrew-science/issues/2337#issuecomment-170011511.

* Re-wrap comment, line length not a problem.

I'd broken a comment across to line in a fit of flake8
induced fear.  Adam pointed out that it's ok.

* Remove explicit prefix config

Remove explicit prefix config, the autotools package does it for us.

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