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-daligner/package.py

@@ -0,0 +1,48 @@
+##############################################################################
+# 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 PacbioDaligner(MakefilePackage):
+    """Daligner: The Dazzler "Overlap" Module. This is a special fork
+       required for some pacbio utilities."""
+
+    homepage = "https://github.com/PacificBiosciences/DALIGNER"
+    url      = "https://github.com/PacificBiosciences/DALIGNER"
+
+    version('2017-08-05',
+            git='https://github.com/PacificBiosciences/DALIGNER.git',
+            commit='0fe5240d2cc6b55bf9e04465b700b76110749c9d')
+
+    depends_on('gmake', type='build')
+    depends_on('pacbio-dazz-db')
+
+    def edit(self, spec, prefix):
+        mkdir(prefix.bin)
+        makefile = FileFilter('Makefile')
+        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)