svn commit: r455154 - in head/biology: . py-cutadapt

[Jason W. Bacon]

Author: jwb
Date: Wed Nov 29 22:17:43 2017
New Revision: 455154
URL: https://svnweb.freebsd.org/changeset/ports/455154

Log:
  [new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po
  ly-A tails, etc
  Approved by: jrm (mentor)
  Differential Revision:  https://reviews.freebsd.org/D13294

Added:
  head/biology/py-cutadapt/
  head/biology/py-cutadapt/Makefile   (contents, props changed)
  head/biology/py-cutadapt/distinfo   (contents, props changed)
  head/biology/py-cutadapt/pkg-descr   (contents, props changed)
  head/biology/py-cutadapt/pkg-plist   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Wed Nov 29 22:15:31 2017	(r455153)
+++ head/biology/Makefile	Wed Nov 29 22:17:43 2017	(r455154)
@@ -85,6 +85,7 @@
     SUBDIR += py-biom-format
     SUBDIR += py-biopython
     SUBDIR += py-bx-python
+    SUBDIR += py-cutadapt
     SUBDIR += py-pysam
     SUBDIR += pycogent
     SUBDIR += pyfasta

Added: head/biology/py-cutadapt/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/py-cutadapt/Makefile	Wed Nov 29 22:17:43 2017	(r455154)
@@ -0,0 +1,23 @@
+# $FreeBSD$
+
+PORTNAME=	cutadapt
+PORTVERSION=	1.14
+CATEGORIES=	biology python
+MASTER_SITES=	CHEESESHOP
+MASTER_SITE_SUBDIR=	source/c/cutadapt
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	jwb at FreeBSD.org
+COMMENT=	Finds and removes adapter sequences, primers, poly-A tails, etc
+
+LICENSE=	MIT
+
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}xopen>0:archivers/py-xopen
+
+USES=		python
+USE_PYTHON=	distutils
+
+post-install:
+	@${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/cutadapt/*.so
+
+.include <bsd.port.mk>

Added: head/biology/py-cutadapt/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/py-cutadapt/distinfo	Wed Nov 29 22:17:43 2017	(r455154)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1509552013
+SHA256 (cutadapt-1.14.tar.gz) = f32990a8b2f8b53f8f4c723ada3d256a8e8476febdd296506764cc8e83397d3d
+SIZE (cutadapt-1.14.tar.gz) = 283631

Added: head/biology/py-cutadapt/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/py-cutadapt/pkg-descr	Wed Nov 29 22:17:43 2017	(r455154)
@@ -0,0 +1,4 @@
+Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
+types of unwanted sequences from your high-throughput sequencing reads.
+
+WWW: https://pypi.python.org/pypi/cutadapt/

Added: head/biology/py-cutadapt/pkg-plist
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/py-cutadapt/pkg-plist	Wed Nov 29 22:17:43 2017	(r455154)
@@ -0,0 +1,43 @@
+bin/cutadapt
+%%PYTHON_SITELIBDIR%%/cutadapt/__init__.py
+%%PYTHON_SITELIBDIR%%/cutadapt/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/__init__.%%PYTHON_PYOEXTENSION%%
+%%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.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/cutadapt/adapters.py
+%%PYTHON_SITELIBDIR%%/cutadapt/adapters.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/adapters.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/cutadapt/align.py
+%%PYTHON_SITELIBDIR%%/cutadapt/align.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/align.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/cutadapt/colorspace.py
+%%PYTHON_SITELIBDIR%%/cutadapt/colorspace.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/colorspace.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/cutadapt/compat.py
+%%PYTHON_SITELIBDIR%%/cutadapt/compat.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/compat.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/cutadapt/filters.py
+%%PYTHON_SITELIBDIR%%/cutadapt/filters.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/filters.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/cutadapt/modifiers.py
+%%PYTHON_SITELIBDIR%%/cutadapt/modifiers.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/modifiers.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/cutadapt/qualtrim.py
+%%PYTHON_SITELIBDIR%%/cutadapt/qualtrim.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/qualtrim.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/cutadapt/report.py
+%%PYTHON_SITELIBDIR%%/cutadapt/report.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/report.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/cutadapt/scripts/__init__.py
+%%PYTHON_SITELIBDIR%%/cutadapt/scripts/__init__.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/scripts/__init__.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/cutadapt/scripts/cutadapt.py
+%%PYTHON_SITELIBDIR%%/cutadapt/scripts/cutadapt.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/scripts/cutadapt.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/cutadapt/seqio.py
+%%PYTHON_SITELIBDIR%%/cutadapt/seqio.pyc
+%%PYTHON_SITELIBDIR%%/cutadapt/seqio.%%PYTHON_PYOEXTENSION%%