Date: Wed, 29 Nov 2017 22:17:44 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r455154 - in head/biology: . py-cutadapt Message-ID: <201711292217.vATMHiQD017439@repo.freebsd.org>
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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@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%%
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