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

7 files changed, 293 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/falcon/package.py b/var/spack/repos/builtin/packages/falcon/package.py
new file mode 100644
index 0000000000..7532e6e8b4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/falcon/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 Falcon(PythonPackage):
+    """Falcon: a set of tools for fast aligning long reads for consensus
+    and assembly.
+
+    The Falcon tool kit is a set of simple code collection which I use
+    for studying efficient assembly algorithm for haploid and diploid genomes.
+    It has some back-end code implemented in C for speed and some simple
+    front-end written in Python for convenience."""
+
+    homepage = "https://github.com/PacificBiosciences/FALCON"
+    url      = "https://github.com/PacificBiosciences/FALCON.git"
+
+    version('2017-05-30',
+            git='https://github.com/PacificBiosciences/FALCON.git',
+            commit='86cec6157291679095ea6080b0cde6561eccc041')
+
+    depends_on('py-setuptools', type='run')
+    depends_on('py-pypeflow', type='run')
+    depends_on('py-networkx@1.7:1.10', type=['build', 'run'])
+    depends_on('pacbio-dazz-db', type='run')
+    depends_on('pacbio-daligner', type='run')
+    depends_on('pacbio-dextractor', type='run')
+    depends_on('pacbio-damasker', type='run')
diff --git a/var/spack/repos/builtin/packages/pacbio-daligner/package.py b/var/spack/repos/builtin/packages/pacbio-daligner/package.py
new file mode 100644
index 0000000000..695c4717f7
--- /dev/null
+++ b/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)
diff --git a/var/spack/repos/builtin/packages/pacbio-damasker/package.py b/var/spack/repos/builtin/packages/pacbio-damasker/package.py
new file mode 100644
index 0000000000..b2415fd340
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pacbio-damasker/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# 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 PacbioDamasker(MakefilePackage):
+    """Damasker: The Dazzler Repeat Masking Suite. This is a special fork
+       required for some pacbio utilities."""
+
+    homepage = "https://github.com/PacificBiosciences/DAMASKER"
+    url      = "https://github.com/PacificBiosciences/DAMASKER"
+
+    version('2017-02-11',
+            git='https://github.com/PacificBiosciences/DAMASKER.git',
+            commit='144244b77d52cb785cb1b3b8ae3ab6f3f0c63264')
+
+    depends_on('gmake', type='build')
+
+    def edit(self, spec, prefix):
+        mkdirp(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)
diff --git a/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py b/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
new file mode 100644
index 0000000000..1223c25f37
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
@@ -0,0 +1,55 @@
+##############################################################################
+# 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 PacbioDazzDb(MakefilePackage):
+    """The Dazzler Database Library. This version is a special fork
+       required for some pacbio utilities."""
+
+    homepage = "https://github.com/PacificBiosciences/DAZZ_DB"
+    url      = "https://github.com/PacificBiosciences/DAZZ_DB"
+
+    version('2017-04-10',
+            git='https://github.com/PacificBiosciences/DAZZ_DB.git',
+            commit='f29d27d51f460563481cd227d17f4bdc5e288365')
+
+    depends_on('gmake', type='build')
+
+    def edit(self, spec, prefix):
+        mkdirp(prefix.bin)
+        mkdirp(prefix.lib)
+        mkdirp(prefix.include)
+        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)
+        gmf.filter('rsync\s*-av\s*libdazzdb.*\s*\$\{PREFIX\}/lib',
+                   'cp libdazzdb.* ' + prefix.lib)
+        gmf.filter(('rsync\s*-av\s*\$\(wildcard\s*\$\{THISDIR\}/\*.h'
+                    '\)\s*\$\{PREFIX\}/include'),
+                   'cp *.h ' + prefix.include)
diff --git a/var/spack/repos/builtin/packages/pacbio-dextractor/package.py b/var/spack/repos/builtin/packages/pacbio-dextractor/package.py
new file mode 100644
index 0000000000..91a4e6f330
--- /dev/null
+++ b/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)
diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py
index 2bdf741049..1d8dfa6b53 100644
--- a/var/spack/repos/builtin/packages/py-networkx/package.py
+++ b/var/spack/repos/builtin/packages/py-networkx/package.py
@@ -32,6 +32,7 @@ class PyNetworkx(PythonPackage):
     url      = "https://pypi.io/packages/source/n/networkx/networkx-1.11.tar.gz"
 
     version('1.11', '6ef584a879e9163013e9a762e1cf7cd1')
+    version('1.10', 'eb7a065e37250a4cc009919dacfe7a9d')
 
     depends_on('py-decorator', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pypeflow/package.py b/var/spack/repos/builtin/packages/py-pypeflow/package.py
new file mode 100644
index 0000000000..8741b731f5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pypeflow/package.py
@@ -0,0 +1,40 @@
+##############################################################################
+# 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 PyPypeflow(PythonPackage):
+    """pypeFLOW is light weight and reusable make / flow data process
+    library written in Python."""
+
+    homepage = "https://github.com/PacificBiosciences/pypeFLOW"
+    url      = "https://github.com/PacificBiosciences/pypeFLOW"
+
+    version('2017-05-04',
+            git='https://github.com/PacificBiosciences/pypeFLOW.git',
+            commit='f23a1b290876bbdf130611000934ae4247158073')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-networkx@1.7:1.11', type=['build', 'run'])