Date: Sat, 6 May 2017 06:07:04 +0000 (UTC) From: Martin Wilke <miwi@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r440232 - in head/biology: . py-bx-python Message-ID: <201705060607.v466747A082752@repo.freebsd.org>
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Author: miwi Date: Sat May 6 06:07:03 2017 New Revision: 440232 URL: https://svnweb.freebsd.org/changeset/ports/440232 Log: 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> Added: head/biology/py-bx-python/ head/biology/py-bx-python/Makefile (contents, props changed) head/biology/py-bx-python/distinfo (contents, props changed) head/biology/py-bx-python/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat May 6 06:05:24 2017 (r440231) +++ head/biology/Makefile Sat May 6 06:07:03 2017 (r440232) @@ -83,6 +83,7 @@ SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython + SUBDIR += py-bx-python SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta Added: head/biology/py-bx-python/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-bx-python/Makefile Sat May 6 06:07:03 2017 (r440232) @@ -0,0 +1,26 @@ +# 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} \ + ${PYTHON_PKGNAMEPREFIX}python-lzo>0:archivers/py-python-lzo +RUN_DEPENDS:= ${BUILD_DEPENDS} + +USE_GITHUB= yes +GH_ACCOUNT= bxlab + +USES= compiler python +USE_PYTHON= autoplist distutils + +.include <bsd.port.mk> Added: head/biology/py-bx-python/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-bx-python/distinfo Sat May 6 06:07:03 2017 (r440232) @@ -0,0 +1,3 @@ +TIMESTAMP = 1492586227 +SHA256 (bxlab-bx-python-v0.7.4_GH0.tar.gz) = 1066d1e56d062d0661f23c19942eb757bd7ab7cb8bc7d89a72fdc3931c995cb4 +SIZE (bxlab-bx-python-v0.7.4_GH0.tar.gz) = 2277893 Added: head/biology/py-bx-python/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-bx-python/pkg-descr Sat May 6 06:07:03 2017 (r440232) @@ -0,0 +1,17 @@ +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
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