adding falcon (#5057)

* py-networkx: adding older version py-networkx

* py-pypeflow: new package

* falcon: adding new package
pacbio-daligner: adding new package
pacbio-damasker: adding new package
pacbio-dazz-db: adding new package
pacbio-dextractor: adding new package

* py-networkx: modifying version order to be in line with convention

* falcon: tweaking py-networkx dependency to satisfy setuptools
py-pypeflow: adding missing dependency

* pacbio-dextractor: changing hdf5 dependency

* pacbio-daligner: adding gmake build dep
pacbio-damasker: adding gmake build dep
pacbio-dazz-db: adding gmake build dep
pacbio-dextractor: adding gmake build dep

var/spack/repos/builtin/packages/pacbio-dextractor/package.py

@@ -0,0 +1,51 @@
+##############################################################################
+# 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 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 PacbioDextractor(MakefilePackage):
+    """The Dextractor and Compression Command Library. This is a special
+       fork required by some pacbio utilities."""
+
+    homepage = "https://github.com/PacificBiosciences/DEXTRACTOR"
+    url      = "https://github.com/PacificBiosciences/DEXTRACTOR"
+
+    version('2016-08-09',
+            git='https://github.com/PacificBiosciences/DEXTRACTOR.git',
+            commit='89726800346d0bed15d98dcc577f4c7733aab4b1')
+
+    depends_on('hdf5')
+    depends_on('gmake', type='build')
+
+    def edit(self, spec, prefix):
+        mkdirp(prefix.bin)
+        makefile = FileFilter('Makefile')
+        makefile.filter('PATH_HDF5\s*=\s*/sw/apps/hdf5/current',
+                        'PATH_HDF5 = ' + spec['hdf5'].prefix)
+        makefile.filter('PATH_HDF5\*s=\s*/usr/local/hdf5', '')
+        makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
+        gmf = FileFilter('GNUmakefile')
+        gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
+                   'cp ${ALL} ' + prefix.bin)