'Add py-pbfalcon: Experimental PacBio diploid assembler'

[Jason Bacon <bacon@centosdev.local>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon@centosdev.local>
Pushed By:	outpaddling
Date:		Thu Mar 30 12:02:02 2017 -0500
Changeset:	c47a532955acac33f2c72ce33b28a09c7e88ad40

Modified Files:
	Makefile
Added Files:
	py-pbfalcon/DESCR
	py-pbfalcon/Makefile
	py-pbfalcon/PLIST
	py-pbfalcon/TODO
	py-pbfalcon/buildlink3.mk
	py-pbfalcon/distinfo
	py-pbfalcon/patches/patch-src_py_run__support.py

Log Message:
'Add py-pbfalcon: 	Experimental PacBio diploid assembler'

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c47a532955acac33f2c72ce33b28a09c7e88ad40

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                                         |  1 +
 py-pbfalcon/DESCR                                |  3 +
 py-pbfalcon/Makefile                             | 54 +++++++++++++
 py-pbfalcon/PLIST                                | 98 ++++++++++++++++++++++++
 py-pbfalcon/TODO                                 |  1 +
 py-pbfalcon/buildlink3.mk                        | 12 +++
 py-pbfalcon/distinfo                             |  7 ++
 py-pbfalcon/patches/patch-src_py_run__support.py | 10 +++
 8 files changed, 186 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 446d38ff59..0395724362 100644
--- a/Makefile
+++ b/Makefile
@@ -3294,6 +3294,7 @@ SUBDIR+=	py-parserutils
 SUBDIR+=	py-path.py
 SUBDIR+=	py-pathlib
 SUBDIR+=	py-pattyrn
+SUBDIR+=	py-pbfalcon
 SUBDIR+=	py-pcapy
 SUBDIR+=	py-pdef
 SUBDIR+=	py-pdfposter
diff --git a/py-pbfalcon/DESCR b/py-pbfalcon/DESCR
new file mode 100644
index 0000000000..a96e4ea576
--- /dev/null
+++ b/py-pbfalcon/DESCR
@@ -0,0 +1,3 @@
+Experimental PacBio diploid assembler.
+
+WWW: https://github.com/PacificBiosciences/FALCON
diff --git a/py-pbfalcon/Makefile b/py-pbfalcon/Makefile
new file mode 100644
index 0000000000..634961d757
--- /dev/null
+++ b/py-pbfalcon/Makefile
@@ -0,0 +1,54 @@
+# $NetBSD$
+
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+# Must use the exact same version of dazz_db, daligner, pypeflow, and falcon!
+# Distfiles are rolled from a FALCON-integrate snapshot to ensure that
+# this is possible.
+# FIXME: Get to a newer version of rdflib and eliminate rdfextras
+# Unknown tool: USE_TOOLS=	python
+#post-stage:
+#	${STRIP_CMD} ${DESTDIR}${PREFIX}/lib/python2.7/site-packages/falcon_kit/*.so
+
+DISTNAME=	pbfalcon-${PORTVERSION}
+PKGNAME=	${PYPKGPREFIX}-pbfalcon-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	http://acadix.biz/Ports/distfiles/
+EXTRACT_SUFX=	.tar.xz
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+
+COMMENT=	Experimental PacBio diploid assembler
+# Double-check this
+LICENSE=	modified-bsd
+
+# Pessimistic assumption.  Test and change if possible.
+MAKE_JOBS_SAFE=	no
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+PYDISTUTILSPKG=	yes
+
+DEPENDS+=	${PYPKGPREFIX}-networkx>=0:../../math/py-networkx
+
+PORTVERSION=	2015.10.28
+
+post-patch:
+	for f in ${WRKSRC}/src/py_scripts/*.py; do \
+		${PRINTF} "#!${PYTHONBIN}\\n\\n" > $$f.temp; \
+		${CAT} $$f >> $$f.temp; \
+		${MV} -f $$f.temp $$f; \
+	done
+
+.include "../../lang/python/distutils.mk"
+.include "../../wip/dazz_db/buildlink3.mk"
+.include "../../wip/daligner/buildlink3.mk"
+.include "../../wip/py-pypeflow/buildlink3.mk"
+.include "../../wip/py-rdflib340/buildlink3.mk"
+.include "../../wip/py-rdfextras/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-pbfalcon/PLIST b/py-pbfalcon/PLIST
new file mode 100644
index 0000000000..4d11c4e6c6
--- /dev/null
+++ b/py-pbfalcon/PLIST
@@ -0,0 +1,98 @@
+@comment $NetBSD$
+bin/falcon-task
+bin/fc_actg_coordinate
+bin/fc_actg_coordinate.py
+bin/fc_consensus
+bin/fc_consensus.py
+bin/fc_contig_annotate
+bin/fc_contig_annotate.py
+bin/fc_ctg_link_analysis
+bin/fc_ctg_link_analysis.py
+bin/fc_dedup_a_tigs
+bin/fc_dedup_a_tigs.py
+bin/fc_graph_to_contig
+bin/fc_graph_to_contig.py
+bin/fc_graph_to_utgs
+bin/fc_graph_to_utgs.py
+bin/fc_ovlp_filter
+bin/fc_ovlp_filter.py
+bin/fc_ovlp_stats
+bin/fc_ovlp_stats.py
+bin/fc_ovlp_to_graph
+bin/fc_ovlp_to_graph.py
+bin/fc_run
+bin/fc_run.py
+${PYSITELIB}/falcon_kit-0.4.0-py2.7.egg-info/dependency_links.txt
+${PYSITELIB}/falcon_kit-0.4.0-py2.7.egg-info/entry_points.txt
+${PYSITELIB}/falcon_kit-0.4.0-py2.7.egg-info/not-zip-safe
+${PYSITELIB}/falcon_kit-0.4.0-py2.7.egg-info/PKG-INFO
+${PYSITELIB}/falcon_kit-0.4.0-py2.7.egg-info/requires.txt
+${PYSITELIB}/falcon_kit-0.4.0-py2.7.egg-info/SOURCES.txt
+${PYSITELIB}/falcon_kit-0.4.0-py2.7.egg-info/top_level.txt
+${PYSITELIB}/falcon_kit/ext_falcon.so
+${PYSITELIB}/falcon_kit/falcon_kit.py
+${PYSITELIB}/falcon_kit/falcon_kit.pyc
+${PYSITELIB}/falcon_kit/falcon_kit.pyo
+${PYSITELIB}/falcon_kit/FastaReader.py
+${PYSITELIB}/falcon_kit/FastaReader.pyc
+${PYSITELIB}/falcon_kit/FastaReader.pyo
+${PYSITELIB}/falcon_kit/fc_asm_graph.py
+${PYSITELIB}/falcon_kit/fc_asm_graph.pyc
+${PYSITELIB}/falcon_kit/fc_asm_graph.pyo
+${PYSITELIB}/falcon_kit/functional.py
+${PYSITELIB}/falcon_kit/functional.pyc
+${PYSITELIB}/falcon_kit/functional.pyo
+${PYSITELIB}/falcon_kit/__init__.py
+${PYSITELIB}/falcon_kit/__init__.pyc
+${PYSITELIB}/falcon_kit/__init__.pyo
+${PYSITELIB}/falcon_kit/mains/actg_coordinate.py
+${PYSITELIB}/falcon_kit/mains/actg_coordinate.pyc
+${PYSITELIB}/falcon_kit/mains/actg_coordinate.pyo
+${PYSITELIB}/falcon_kit/mains/consensus.py
+${PYSITELIB}/falcon_kit/mains/consensus.pyc
+${PYSITELIB}/falcon_kit/mains/consensus.pyo
+${PYSITELIB}/falcon_kit/mains/contig_annotate.py
+${PYSITELIB}/falcon_kit/mains/contig_annotate.pyc
+${PYSITELIB}/falcon_kit/mains/contig_annotate.pyo
+${PYSITELIB}/falcon_kit/mains/ctg_link_analysis.py
+${PYSITELIB}/falcon_kit/mains/ctg_link_analysis.pyc
+${PYSITELIB}/falcon_kit/mains/ctg_link_analysis.pyo
+${PYSITELIB}/falcon_kit/mains/dedup_a_tigs.py
+${PYSITELIB}/falcon_kit/mains/dedup_a_tigs.pyc
+${PYSITELIB}/falcon_kit/mains/dedup_a_tigs.pyo
+${PYSITELIB}/falcon_kit/mains/graph_to_contig.py
+${PYSITELIB}/falcon_kit/mains/graph_to_contig.pyc
+${PYSITELIB}/falcon_kit/mains/graph_to_contig.pyo
+${PYSITELIB}/falcon_kit/mains/graph_to_utgs.py
+${PYSITELIB}/falcon_kit/mains/graph_to_utgs.pyc
+${PYSITELIB}/falcon_kit/mains/graph_to_utgs.pyo
+${PYSITELIB}/falcon_kit/mains/__init__.py
+${PYSITELIB}/falcon_kit/mains/__init__.pyc
+${PYSITELIB}/falcon_kit/mains/__init__.pyo
+${PYSITELIB}/falcon_kit/mains/ovlp_filter.py
+${PYSITELIB}/falcon_kit/mains/ovlp_filter.pyc
+${PYSITELIB}/falcon_kit/mains/ovlp_filter.pyo
+${PYSITELIB}/falcon_kit/mains/ovlp_stats.py
+${PYSITELIB}/falcon_kit/mains/ovlp_stats.pyc
+${PYSITELIB}/falcon_kit/mains/ovlp_stats.pyo
+${PYSITELIB}/falcon_kit/mains/ovlp_to_graph.py
+${PYSITELIB}/falcon_kit/mains/ovlp_to_graph.pyc
+${PYSITELIB}/falcon_kit/mains/ovlp_to_graph.pyo
+${PYSITELIB}/falcon_kit/mains/run.py
+${PYSITELIB}/falcon_kit/mains/run.pyc
+${PYSITELIB}/falcon_kit/mains/run.pyo
+${PYSITELIB}/falcon_kit/mains/tasks.py
+${PYSITELIB}/falcon_kit/mains/tasks.pyc
+${PYSITELIB}/falcon_kit/mains/tasks.pyo
+${PYSITELIB}/falcon_kit/multiproc.py
+${PYSITELIB}/falcon_kit/multiproc.pyc
+${PYSITELIB}/falcon_kit/multiproc.pyo
+${PYSITELIB}/falcon_kit/run_support.py
+${PYSITELIB}/falcon_kit/run_support.pyc
+${PYSITELIB}/falcon_kit/run_support.pyo
+${PYSITELIB}/falcon_kit/util/__init__.py
+${PYSITELIB}/falcon_kit/util/__init__.pyc
+${PYSITELIB}/falcon_kit/util/__init__.pyo
+${PYSITELIB}/falcon_kit/util/io.py
+${PYSITELIB}/falcon_kit/util/io.pyc
+${PYSITELIB}/falcon_kit/util/io.pyo
diff --git a/py-pbfalcon/TODO b/py-pbfalcon/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/py-pbfalcon/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/py-pbfalcon/buildlink3.mk b/py-pbfalcon/buildlink3.mk
new file mode 100644
index 0000000000..30e422168d
--- /dev/null
+++ b/py-pbfalcon/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	py27-pbfalcon
+
+.if !defined(PY27_PBFALCON_BUILDLINK3_MK)
+PY27_PBFALCON_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.py27-pbfalcon+=	py27-pbfalcon>=2015.08.17
+BUILDLINK_PKGSRCDIR.py27-pbfalcon?=	../../wip/py-pbfalcon
+.endif	# PY27_PBFALCON_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-py27-pbfalcon
diff --git a/py-pbfalcon/distinfo b/py-pbfalcon/distinfo
new file mode 100644
index 0000000000..b8b2cfd118
--- /dev/null
+++ b/py-pbfalcon/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (pbfalcon-2015.10.28.tar.xz) = 972b95e543a4b32c8965cbb1b09968cde6281b81
+RMD160 (pbfalcon-2015.10.28.tar.xz) = e042a996fe813ec468974458e13631cb1c76d310
+SHA512 (pbfalcon-2015.10.28.tar.xz) = 464f1730d283be11b1aeea0ff9be98d85dbb2ec313dcdf53a9a3337790d6814a11b9d8979abf3669f1ba379c68bb1612dbe18ae9ad4a5764ef0c75aff67938dd
+Size (pbfalcon-2015.10.28.tar.xz) = 458572 bytes
+SHA1 (patch-src_py_run__support.py) = 49621ce5cdd1907c03fd91d7afdf5a978944d7db
diff --git a/py-pbfalcon/patches/patch-src_py_run__support.py b/py-pbfalcon/patches/patch-src_py_run__support.py
new file mode 100644
index 0000000000..711b17ccdf
--- /dev/null
+++ b/py-pbfalcon/patches/patch-src_py_run__support.py
@@ -0,0 +1,10 @@
+--- src/py/run_support.py.orig	2015-10-28 12:31:41.000000000 -0500
++++ src/py/run_support.py	2015-10-28 12:32:00.000000000 -0500
+@@ -33,6 +33,7 @@
+         content = ifs.read()
+     content = _prepend_env_paths(content, names)
+     with open(fn, 'w') as ofs:
++        ofs.write('#!/usr/bin/env bash\n\n')
+         ofs.write(content)
+ 
+ def use_tmpdir_for_files(basenames, src_dir, link_dir):