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Index: head/biology/py-cutadapt/Makefile
===================================================================
--- head/biology/py-cutadapt/Makefile
+++ head/biology/py-cutadapt/Makefile
@@ -1,20 +1,22 @@
# $FreeBSD$
PORTNAME= cutadapt
-PORTVERSION= 1.14
+PORTVERSION= 1.18
CATEGORIES= biology python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= jwb@FreeBSD.org
-COMMENT= Finds and removes adapter sequences, primers, poly-A tails, etc
+COMMENT= Trim adapters from high-throughput sequencing reads
LICENSE= MIT
+LICENSE_FILE= ${WRKSRC}/LICENSE
-RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}xopen>0:archivers/py-xopen@${PY_FLAVOR}
+RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}xopen>=0.3.2:archivers/py-xopen@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}bz2file>=0.98:archivers/py-bz2file@${PY_FLAVOR}
USES= python
-USE_PYTHON= distutils py3kplist
+USE_PYTHON= autoplist concurrent distutils
post-install:
@${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/cutadapt/*.so
Index: head/biology/py-cutadapt/distinfo
===================================================================
--- head/biology/py-cutadapt/distinfo
+++ head/biology/py-cutadapt/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1509552013
-SHA256 (cutadapt-1.14.tar.gz) = f32990a8b2f8b53f8f4c723ada3d256a8e8476febdd296506764cc8e83397d3d
-SIZE (cutadapt-1.14.tar.gz) = 283631
+TIMESTAMP = 1536508727
+SHA256 (cutadapt-1.18.tar.gz) = 17aabf9b19d09a426d96030a83ad003c97b26dba9d45bf5570d33088fcd533f9
+SIZE (cutadapt-1.18.tar.gz) = 342050
Index: head/biology/py-cutadapt/pkg-plist
===================================================================
--- head/biology/py-cutadapt/pkg-plist
+++ head/biology/py-cutadapt/pkg-plist
@@ -1,43 +0,0 @@
-bin/cutadapt
-%%PYTHON_SITELIBDIR%%/cutadapt/__init__.py
-%%PYTHON_SITELIBDIR%%/cutadapt/__init__.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/__init__.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/_align.so
-%%PYTHON_SITELIBDIR%%/cutadapt/_qualtrim.so
-%%PYTHON_SITELIBDIR%%/cutadapt/_seqio.so
-%%PYTHON_SITELIBDIR%%/cutadapt/_version.py
-%%PYTHON_SITELIBDIR%%/cutadapt/_version.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/_version.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/adapters.py
-%%PYTHON_SITELIBDIR%%/cutadapt/adapters.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/adapters.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/align.py
-%%PYTHON_SITELIBDIR%%/cutadapt/align.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/align.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/colorspace.py
-%%PYTHON_SITELIBDIR%%/cutadapt/colorspace.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/colorspace.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/compat.py
-%%PYTHON_SITELIBDIR%%/cutadapt/compat.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/compat.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/filters.py
-%%PYTHON_SITELIBDIR%%/cutadapt/filters.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/filters.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/modifiers.py
-%%PYTHON_SITELIBDIR%%/cutadapt/modifiers.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/modifiers.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/qualtrim.py
-%%PYTHON_SITELIBDIR%%/cutadapt/qualtrim.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/qualtrim.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/report.py
-%%PYTHON_SITELIBDIR%%/cutadapt/report.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/report.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/scripts/__init__.py
-%%PYTHON_SITELIBDIR%%/cutadapt/scripts/__init__.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/scripts/__init__.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/scripts/cutadapt.py
-%%PYTHON_SITELIBDIR%%/cutadapt/scripts/cutadapt.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/scripts/cutadapt.pyo
-%%PYTHON_SITELIBDIR%%/cutadapt/seqio.py
-%%PYTHON_SITELIBDIR%%/cutadapt/seqio.pyc
-%%PYTHON_SITELIBDIR%%/cutadapt/seqio.pyo

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