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freebsd-ports/biology/pycogent/Makefile

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- Update to 1.5.3 - Trim Makefile headers
2012-10-08 05:17:02 +02:00
# Created by: Wen Heping <wenheping@gmail.com>
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/ PR: ports/135863 Submitted by: Wen Heping <wenheping at gmail.com>
2009-06-22 14:46:56 +02:00
# $FreeBSD$
PORTNAME= pycogent
- Update to 1.5.3 - Trim Makefile headers
2012-10-08 05:17:02 +02:00
PORTVERSION= 1.5.3
Update to libmpc version 1.0.1 which brings the following fixes: - Switched to automake 1.11.6, see CVE-2012-3386. - #14669: Fixed extraction of CC from gmp.h. - Fixed case of intermediate zero real or imaginary part in mpc_fma, found by hydra with GMP_CHECK_RANDOMIZE=1346362345. This is on top of the following changes from version 1.0 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no invariant sections) for the documentation. - 100% of all lines are covered by tests - Renamed functions . mpc_mul_2exp to mpc_mul_2ui . mpc_div_2exp to mpc_div_2ui - 0^0, which returned (NaN,NaN) previously, now returns (1,+0). - Removed compatibility with K&R compilers, which was untestable due to lack of such compilers. - New functions . mpc_log10 . mpc_mul_2si, mpc_div_2si - Speed-ups . mpc_fma - Bug fixes . mpc_div and mpc_norm now return a value indicating the effective rounding direction, as the other functions. . mpc_mul, mpc_sqr and mpc_norm now return correct results even if there are over- or underflows during the computation. . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has infinite part and equals output variable is corrected. . mpc_fr_sub: Wrong return value for imaginary part is corrected. Convert to the new LIB_DEPENDS standard and remove hard-coded .so versions from a couple of dependent ports. Bump PORTREVISIONS of all dependent ports. PR: 183141 Approved by: portmgr (bdrewery)
2013-10-26 02:52:33 +02:00
PORTREVISION= 1
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/ PR: ports/135863 Submitted by: Wen Heping <wenheping at gmail.com>
2009-06-22 14:46:56 +02:00
CATEGORIES= biology python
- Switch SourceForge ports to the new File Release System: categories starting with B,C
2009-08-22 02:15:15 +02:00
MASTER_SITES= SF/${PORTNAME}/PyCogent/${PORTVERSION}
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/ PR: ports/135863 Submitted by: Wen Heping <wenheping at gmail.com>
2009-06-22 14:46:56 +02:00
DISTNAME= PyCogent-${PORTVERSION}
EXTRACT_SUFX= .tgz
- Update to 1.4 - Update my mail address to FreeBSD
2009-12-17 07:51:53 +01:00
MAINTAINER= wen@FreeBSD.org
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/ PR: ports/135863 Submitted by: Wen Heping <wenheping at gmail.com>
2009-06-22 14:46:56 +02:00
COMMENT= A toolkit for statistical analysis of biological sequences
BUILD_DEPENDS= ${PYNUMPY} \
${LOCALBASE}/bin/cython:${PORTSDIR}/lang/cython \
${LOCALBASE}/bin/sphinx-build:${PORTSDIR}/textproc/py-sphinx \
- Fix *_DEPENDS after the repocopy of databases/py-sqlalchemy (This port doesn't yet support SQLAlchemy 0.7.X) - Bump PORTREVISION
2011-06-25 09:21:20 +02:00
${PYTHON_PKGNAMEPREFIX}sqlalchemy06>=0.5:${PORTSDIR}/databases/py-sqlalchemy06
- Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or RUN_DEPENDS=${BUILD_DEPENDS} to use := which portlint has warned about for a while. PR: ports/168208 Approved by: portmgr (miwi)
2012-06-10 20:42:48 +02:00
RUN_DEPENDS:= ${BUILD_DEPENDS}
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/ PR: ports/135863 Submitted by: Wen Heping <wenheping at gmail.com>
2009-06-22 14:46:56 +02:00
USE_PYTHON= yes
USE_PYDISTUTILS= yes
PYDISTUTILS_PKGNAME= cogent
Add NO_STAGE all over the place in preparation for the staging support (cat: biology)
2013-09-20 17:55:44 +02:00
NO_STAGE= yes
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/ PR: ports/135863 Submitted by: Wen Heping <wenheping at gmail.com>
2009-06-22 14:46:56 +02:00
.include <bsd.port.mk>
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