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Date:      Sat, 6 May 2017 06:05:24 +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: r440231 - in head/biology: . py-pysam py-pysam/files
Message-ID:  <201705060605.v4665OPM082472@repo.freebsd.org>

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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 <yuri@rawbw.com>

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 <yuri@rawbw.com>
+# $FreeBSD$
+
+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 <bsd.port.mk>

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



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