svn commit: r440231 - in head/biology: . py-pysam py-pysam/files
Martin Wilke
miwi at FreeBSD.org
Sat May 6 06:05:26 UTC 2017
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 at 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 at rawbw.com>
+# $FreeBSD$
+
+PORTNAME= pysam
+PORTVERSION= 0.11
+CATEGORIES= biology python
+MASTER_SITES= CHEESESHOP
+PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER= yuri at 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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