Date: Sat, 20 Jun 2009 13:45:40 GMT From: Wen Heping <wenheping@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/135863: [NEW PORT]biology/pycogent:A toolkit for statistical analysis of biological sequences Message-ID: <200906201345.n5KDje3N028786@www.freebsd.org> Resent-Message-ID: <200906201350.n5KDo3SL061900@freefall.freebsd.org>
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>Number: 135863 >Category: ports >Synopsis: [NEW PORT]biology/pycogent:A toolkit for statistical analysis of biological sequences >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Sat Jun 20 13:50:03 UTC 2009 >Closed-Date: >Last-Modified: >Originator: Wen Heping >Release: FreeBSD 8.0-CURRENT >Organization: ChangAn Middle School >Environment: FreeBSD fb8.wenjing.com 8.0-CURRENT FreeBSD 8.0-CURRENT #0: Sun Mar 22 22:12:06 CST 2009 root@fb8.wenjing.com:/usr/obj/usr/src/sys/GENERIC i386 >Description: PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data. WWW: http://pycogent.sourceforge.net/ >How-To-Repeat: >Fix: Patch attached with submission follows: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # pycogent # pycogent/Makefile # pycogent/distinfo # pycogent/pkg-descr # pycogent/pkg-plist # echo c - pycogent mkdir -p pycogent > /dev/null 2>&1 echo x - pycogent/Makefile sed 's/^X//' >pycogent/Makefile << '75b6d9d52a590046a885ebab70b8caf4' X# New ports collection makefile for: pycogent X# Date created: 20 June, 2009 X# Whom: Wen Heping <wenheping@gmail.com> X# X# $FreeBSD$ X# X XPORTNAME= pycogent XPORTVERSION= 1.3.1 XCATEGORIES= biology python XMASTER_SITES= SF XDISTNAME= PyCogent-${PORTVERSION} XEXTRACT_SUFX= .tgz X XMAINTAINER= wenheping@gmail.com XCOMMENT= A toolkit for statistical analysis of biological sequences X XBUILD_DEPENDS= ${PYNUMPY} \ X ${LOCALBASE}/bin/cython:${PORTSDIR}/lang/cython \ X ${LOCALBASE}/bin/sphinx-build:${PORTSDIR}/textproc/py-sphinx \ X ${PYTHON_PKGNAMEPREFIX}sqlalchemy>=0.5:${PORTSDIR}/databases/py-sqlalchemy XRUN_DEPENDS= ${BUILD_DEPENDS} X XUSE_PYTHON= yes XUSE_PYDISTUTILS= yes XPYDISTUTILS_PKGNAME= cogent X X.include <bsd.port.mk> 75b6d9d52a590046a885ebab70b8caf4 echo x - pycogent/distinfo sed 's/^X//' >pycogent/distinfo << 'e4e6cbd5a9ee9db6f60e5e3f452bfa0f' XMD5 (PyCogent-1.3.1.tgz) = 4cc108a69e5ffd343508db4615514b74 XSHA256 (PyCogent-1.3.1.tgz) = 56636a2aeee464968056458f8384262f874cdac12b89a43c4c3e5d88582a7fc6 XSIZE (PyCogent-1.3.1.tgz) = 2062874 e4e6cbd5a9ee9db6f60e5e3f452bfa0f echo x - pycogent/pkg-descr sed 's/^X//' >pycogent/pkg-descr << '39f14c750cb59f4eb8126d2c49207b4f' XPyCogent is a software library for genomic biology. It is a fully integrated Xand thoroughly tested framework for: controlling third-party applications; Xdevising workflows; querying databases; conducting novel probabilistic Xanalyses of biological sequence evolution; and generating publication quality Xgraphics. It is distinguished by many unique built-in capabilities (such as Xtrue codon alignment) and the frequent addition of entirely new methods for Xthe analysis of genomic data. X XWWW: http://pycogent.sourceforge.net/ 39f14c750cb59f4eb8126d2c49207b4f echo x - pycogent/pkg-plist sed 's/^X//' >pycogent/pkg-plist << '57a008b0ebd7f436ef4637679dbbc9dd' X%%PYTHON_SITELIBDIR%%/cogent/__init__.py X%%PYTHON_SITELIBDIR%%/cogent/__init__.pyc X%%PYTHON_SITELIBDIR%%/cogent/__init__.pyo X%%PYTHON_SITELIBDIR%%/cogent/align/__init__.py X%%PYTHON_SITELIBDIR%%/cogent/align/__init__.pyc X%%PYTHON_SITELIBDIR%%/cogent/align/__init__.pyo X%%PYTHON_SITELIBDIR%%/cogent/align/_compare.so X%%PYTHON_SITELIBDIR%%/cogent/align/_pairwise_pogs.so X%%PYTHON_SITELIBDIR%%/cogent/align/_pairwise_seqs.so X%%PYTHON_SITELIBDIR%%/cogent/align/algorithm.py X%%PYTHON_SITELIBDIR%%/cogent/align/algorithm.pyc X%%PYTHON_SITELIBDIR%%/cogent/align/algorithm.pyo X%%PYTHON_SITELIBDIR%%/cogent/align/align.py X%%PYTHON_SITELIBDIR%%/cogent/align/align.pyc X%%PYTHON_SITELIBDIR%%/cogent/align/align.pyo X%%PYTHON_SITELIBDIR%%/cogent/align/dp_calculation.py X%%PYTHON_SITELIBDIR%%/cogent/align/dp_calculation.pyc 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%%PYTHON_SITELIBDIR%%/cogent/util X@dirrm %%PYTHON_SITELIBDIR%%/cogent/ 57a008b0ebd7f436ef4637679dbbc9dd exit >Release-Note: >Audit-Trail: >Unformatted:
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