svn commit: r440232 - in head/biology: . py-bx-python
Martin Wilke
miwi at FreeBSD.org
Sat May 6 06:07:05 UTC 2017
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 at 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 at rawbw.com>
+# $FreeBSD$
+
+PORTNAME= bx-python
+PORTVERSION= 0.7.4
+DISTVERSIONPREFIX= v
+CATEGORIES= biology python
+PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER= yuri at 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
More information about the svn-ports-all
mailing list