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pysam is a lightweight wrapper of the htslib C-API and provides facilities to

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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>
This commit is contained in:
Martin Wilke 2017-05-06 06:05:24 +00:00
parent a2c4a5c233
commit 9ca211c1ff
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=440231
5 changed files with 47 additions and 0 deletions
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1
biology/Makefile
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@ -83,6 +83,7 @@
SUBDIR += psi88
SUBDIR += py-biom-format
SUBDIR += py-biopython
SUBDIR += py-pysam
SUBDIR += pycogent
SUBDIR += pyfasta
SUBDIR += python-nexus

22
biology/py-pysam/Makefile Normal file
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@ -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>

3
biology/py-pysam/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1492580723
SHA256 (pysam-0.11.tar.gz) = 815c8a6150c5fe21df227e730dd57e4212984ae568854fcc5873e243072dcbad
SIZE (pysam-0.11.tar.gz) = 2425484

11
biology/py-pysam/files/patch-setup.py Normal file
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@ -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")

10
biology/py-pysam/pkg-descr Normal file
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@ -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