Add py-cutadapt: Finds and removes adapter sequences, primers, poly-A tails, etc

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Fri Nov 3 11:35:58 2017 -0500
Changeset:	e73d0bfa596b17e4226593362c5a483fa5e9e94c

Modified Files:
	Makefile
Added Files:
	py-cutadapt/DESCR
	py-cutadapt/Makefile
	py-cutadapt/PLIST
	py-cutadapt/TODO
	py-cutadapt/buildlink3.mk
	py-cutadapt/distinfo

Log Message:
Add py-cutadapt: 	Finds and removes adapter sequences, primers, poly-A tails, etc

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e73d0bfa596b17e4226593362c5a483fa5e9e94c

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

diffstat:
 Makefile                  |  1 +
 py-cutadapt/DESCR         |  4 ++++
 py-cutadapt/Makefile      | 23 ++++++++++++++++++++++
 py-cutadapt/PLIST         | 50 +++++++++++++++++++++++++++++++++++++++++++++++
 py-cutadapt/TODO          |  1 +
 py-cutadapt/buildlink3.mk | 12 ++++++++++++
 py-cutadapt/distinfo      |  6 ++++++
 7 files changed, 97 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index b016fcbe8c..9912ebf596 100644
--- a/Makefile
+++ b/Makefile
@@ -2972,6 +2972,7 @@ SUBDIR+=	py-cse
 SUBDIR+=	py-csp
 SUBDIR+=	py-ctutils
 SUBDIR+=	py-cubicweb
+SUBDIR+=	py-cutadapt
 SUBDIR+=	py-cva
 SUBDIR+=	py-cvf
 SUBDIR+=	py-cvxpy
diff --git a/py-cutadapt/DESCR b/py-cutadapt/DESCR
new file mode 100644
index 0000000000..044b13c3cf
--- /dev/null
+++ b/py-cutadapt/DESCR
@@ -0,0 +1,4 @@
+Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
+types of unwanted sequence from your high-throughput sequencing reads.
+
+WWW: https://pypi.python.org/pypi/cutadapt/
diff --git a/py-cutadapt/Makefile b/py-cutadapt/Makefile
new file mode 100644
index 0000000000..606fc811b9
--- /dev/null
+++ b/py-cutadapt/Makefile
@@ -0,0 +1,23 @@
+# $NetBSD$
+
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+DISTNAME=	cutadapt-${PORTVERSION}
+PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_PYPI:=c/cutadapt/}
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+
+COMMENT=	Finds and removes adapter sequences, primers, poly-A tails, etc
+LICENSE=	mit
+
+USE_LANGUAGES=	c
+PYDISTUTILSPKG=	yes
+
+PORTVERSION=	1.14
+
+.include "../../lang/python/egg.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-cutadapt/PLIST b/py-cutadapt/PLIST
new file mode 100644
index 0000000000..b8a188efe4
--- /dev/null
+++ b/py-cutadapt/PLIST
@@ -0,0 +1,50 @@
+@comment $NetBSD$
+bin/cutadapt
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/cutadapt/__init__.py
+${PYSITELIB}/cutadapt/__init__.pyc
+${PYSITELIB}/cutadapt/__init__.pyo
+${PYSITELIB}/cutadapt/_align.so
+${PYSITELIB}/cutadapt/_qualtrim.so
+${PYSITELIB}/cutadapt/_seqio.so
+${PYSITELIB}/cutadapt/_version.py
+${PYSITELIB}/cutadapt/_version.pyc
+${PYSITELIB}/cutadapt/_version.pyo
+${PYSITELIB}/cutadapt/adapters.py
+${PYSITELIB}/cutadapt/adapters.pyc
+${PYSITELIB}/cutadapt/adapters.pyo
+${PYSITELIB}/cutadapt/align.py
+${PYSITELIB}/cutadapt/align.pyc
+${PYSITELIB}/cutadapt/align.pyo
+${PYSITELIB}/cutadapt/colorspace.py
+${PYSITELIB}/cutadapt/colorspace.pyc
+${PYSITELIB}/cutadapt/colorspace.pyo
+${PYSITELIB}/cutadapt/compat.py
+${PYSITELIB}/cutadapt/compat.pyc
+${PYSITELIB}/cutadapt/compat.pyo
+${PYSITELIB}/cutadapt/filters.py
+${PYSITELIB}/cutadapt/filters.pyc
+${PYSITELIB}/cutadapt/filters.pyo
+${PYSITELIB}/cutadapt/modifiers.py
+${PYSITELIB}/cutadapt/modifiers.pyc
+${PYSITELIB}/cutadapt/modifiers.pyo
+${PYSITELIB}/cutadapt/qualtrim.py
+${PYSITELIB}/cutadapt/qualtrim.pyc
+${PYSITELIB}/cutadapt/qualtrim.pyo
+${PYSITELIB}/cutadapt/report.py
+${PYSITELIB}/cutadapt/report.pyc
+${PYSITELIB}/cutadapt/report.pyo
+${PYSITELIB}/cutadapt/scripts/__init__.py
+${PYSITELIB}/cutadapt/scripts/__init__.pyc
+${PYSITELIB}/cutadapt/scripts/__init__.pyo
+${PYSITELIB}/cutadapt/scripts/cutadapt.py
+${PYSITELIB}/cutadapt/scripts/cutadapt.pyc
+${PYSITELIB}/cutadapt/scripts/cutadapt.pyo
+${PYSITELIB}/cutadapt/seqio.py
+${PYSITELIB}/cutadapt/seqio.pyc
+${PYSITELIB}/cutadapt/seqio.pyo
diff --git a/py-cutadapt/TODO b/py-cutadapt/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/py-cutadapt/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/py-cutadapt/buildlink3.mk b/py-cutadapt/buildlink3.mk
new file mode 100644
index 0000000000..d529ceeff8
--- /dev/null
+++ b/py-cutadapt/buildlink3.mk
@@ -0,0 +1,12 @@
+# $NetBSD$
+
+BUILDLINK_TREE+=	cutadapt
+
+.if !defined(CUTADAPT_BUILDLINK3_MK)
+CUTADAPT_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.cutadapt+=	cutadapt>=1.8.3
+BUILDLINK_PKGSRCDIR.cutadapt?=	../../wip/py-cutadapt
+.endif	# CUTADAPT_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-cutadapt
diff --git a/py-cutadapt/distinfo b/py-cutadapt/distinfo
new file mode 100644
index 0000000000..6d9b648a89
--- /dev/null
+++ b/py-cutadapt/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (cutadapt-1.14.tar.gz) = cffd036c46e1c159fee6b0da23b175499023de37
+RMD160 (cutadapt-1.14.tar.gz) = 591f69a597f04a04a09538cb67d832a838d5a404
+SHA512 (cutadapt-1.14.tar.gz) = 22028c586801293e1942525f343ee72e590f8a10a3244e9aaadaded45a6f4e126f66d0fd6a6aa821b70d36a9735b7cc74f6582f9fe13b6273387f9d917d55a43
+Size (cutadapt-1.14.tar.gz) = 283631 bytes