From owner-svn-ports-all@freebsd.org Sat May 6 06:05:26 2017 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 4B9A9D603B7; Sat, 6 May 2017 06:05:26 +0000 (UTC) (envelope-from miwi@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 23AC019C7; Sat, 6 May 2017 06:05:26 +0000 (UTC) (envelope-from miwi@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id v4665PdA082477; Sat, 6 May 2017 06:05:25 GMT (envelope-from miwi@FreeBSD.org) Received: (from miwi@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id v4665OPM082472; Sat, 6 May 2017 06:05:24 GMT (envelope-from miwi@FreeBSD.org) Message-Id: <201705060605.v4665OPM082472@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: miwi set sender to miwi@FreeBSD.org using -f From: Martin Wilke Date: Sat, 6 May 2017 06:05:24 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r440231 - in head/biology: . py-pysam py-pysam/files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 06 May 2017 06:05:26 -0000 Author: miwi Date: Sat May 6 06:05:24 2017 New Revision: 440231 URL: https://svnweb.freebsd.org/changeset/ports/440231 Log: pysam is a lightweight wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing. This module provides a low-level wrapper around the htslib C-API as using cython and a high-level API for convenient access to the data within standard genomic file formats. WWW: https://pypi.python.org/pypi/pysam PR: 218745 Submitted by: Yuri Victorovich Added: head/biology/py-pysam/ head/biology/py-pysam/Makefile (contents, props changed) head/biology/py-pysam/distinfo (contents, props changed) head/biology/py-pysam/files/ head/biology/py-pysam/files/patch-setup.py (contents, props changed) head/biology/py-pysam/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat May 6 06:03:58 2017 (r440230) +++ head/biology/Makefile Sat May 6 06:05:24 2017 (r440231) @@ -83,6 +83,7 @@ SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython + SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus Added: head/biology/py-pysam/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-pysam/Makefile Sat May 6 06:05:24 2017 (r440231) @@ -0,0 +1,22 @@ +# Created by: Yuri Victorovich +# $FreeBSD$ + +PORTNAME= pysam +PORTVERSION= 0.11 +CATEGORIES= biology python +MASTER_SITES= CHEESESHOP +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@rawbw.com +COMMENT= Python module for reading, manipulating and writing genomic data sets + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/COPYING + +BUILD_DEPENDS= cython:lang/cython +RUN_DEPENDS= cython:lang/cython + +USES= gmake python:2 +USE_PYTHON= autoplist distutils + +.include Added: head/biology/py-pysam/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-pysam/distinfo Sat May 6 06:05:24 2017 (r440231) @@ -0,0 +1,3 @@ +TIMESTAMP = 1492580723 +SHA256 (pysam-0.11.tar.gz) = 815c8a6150c5fe21df227e730dd57e4212984ae568854fcc5873e243072dcbad +SIZE (pysam-0.11.tar.gz) = 2425484 Added: head/biology/py-pysam/files/patch-setup.py ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-pysam/files/patch-setup.py Sat May 6 06:05:24 2017 (r440231) @@ -0,0 +1,11 @@ +--- setup.py.orig 2017-04-19 05:48:10 UTC ++++ setup.py +@@ -60,7 +60,7 @@ def run_configure(option): + + + def run_make_print_config(): +- stdout = subprocess.check_output(["make", "-s", "print-config"]) ++ stdout = subprocess.check_output(["gmake", "-s", "print-config"]) + if IS_PYTHON3: + stdout = stdout.decode("ascii") + Added: head/biology/py-pysam/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-pysam/pkg-descr Sat May 6 06:05:24 2017 (r440231) @@ -0,0 +1,10 @@ +pysam is a lightweight wrapper of the htslib C-API and provides facilities to +read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access +to the command line functionality of the samtools and bcftools packages. The +module supports compression and random access through indexing. + +This module provides a low-level wrapper around the htslib C-API as using +cython and a high-level API for convenient access to the data within standard +genomic file formats. + +WWW: https://pypi.python.org/pypi/pysam