diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/py-bx-python/Makefile | 26 | ||||
| -rw-r--r-- | biology/py-bx-python/distinfo | 3 | ||||
| -rw-r--r-- | biology/py-bx-python/pkg-descr | 17 |
4 files changed, 47 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 85155f710443..6732768052c0 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -83,6 +83,7 @@ SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython + SUBDIR += py-bx-python SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta diff --git a/biology/py-bx-python/Makefile b/biology/py-bx-python/Makefile new file mode 100644 index 000000000000..89ccb9749a3e --- /dev/null +++ b/biology/py-bx-python/Makefile @@ -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> diff --git a/biology/py-bx-python/distinfo b/biology/py-bx-python/distinfo new file mode 100644 index 000000000000..65e3ff91b1fd --- /dev/null +++ b/biology/py-bx-python/distinfo @@ -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 diff --git a/biology/py-bx-python/pkg-descr b/biology/py-bx-python/pkg-descr new file mode 100644 index 000000000000..b5bab083ebcc --- /dev/null +++ b/biology/py-bx-python/pkg-descr @@ -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 |