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freebsd-ports/biology/py-bx-python/Makefile

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bx-python is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats). Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems). Data structures for working with intervals on sequences: * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation WWW: https://github.com/bxlab/bx-python PR: 218757 Submitted by: Yuri Victorovich <yuri@rawbw.com>
2017-05-06 08:07:03 +02:00
# Created by: Yuri Victorovich <yuri@rawbw.com>
# $FreeBSD$
PORTNAME= bx-python
PORTVERSION= 0.7.4
DISTVERSIONPREFIX= v
CATEGORIES= biology python
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= yuri@rawbw.com
COMMENT= Python module for reading, manipulating and writing genomic data sets
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= ${PYNUMPY} \
Convert Python ports to FLAVORS. Ports using USE_PYTHON=distutils are now flavored. They will automatically get flavors (py27, py34, py35, py36) depending on what versions they support. There is also a USE_PYTHON=flavors for ports that do not use distutils but need FLAVORS to be set. A USE_PYTHON=noflavors can be set if using distutils but flavors are not wanted. A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been added to cope with Python ports that did not have the Python PKGNAMEPREFIX but are flavored. USES=python now also exports a PY_FLAVOR variable that contains the current python flavor. It can be used in dependency lines when the port itself is not python flavored. For example, deskutils/calibre. By default, all the flavors are generated. To only generate flavors for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf. In all the ports with Python dependencies, the *_DEPENDS entries MUST end with the flavor so that the framework knows which to build/use. This is done by appending '@${PY_FLAVOR}' after the origin (or @${FLAVOR} if in a Python module with Python flavors, as the content will be the same). For example: RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} PR: 223071 Reviewed by: portmgr, python Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D12464
2017-11-30 16:50:30 +01:00
${PYTHON_PKGNAMEPREFIX}python-lzo>0:archivers/py-python-lzo@${FLAVOR}
bx-python is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats). Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems). Data structures for working with intervals on sequences: * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation WWW: https://github.com/bxlab/bx-python PR: 218757 Submitted by: Yuri Victorovich <yuri@rawbw.com>
2017-05-06 08:07:03 +02:00
RUN_DEPENDS:= ${BUILD_DEPENDS}
USE_GITHUB= yes
GH_ACCOUNT= bxlab
USES= compiler python
USE_PYTHON= autoplist distutils
.include <bsd.port.mk>
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