diff options
| author | miwi <miwi@FreeBSD.org> | 2017-05-06 14:05:24 +0800 |
|---|---|---|
| committer | miwi <miwi@FreeBSD.org> | 2017-05-06 14:05:24 +0800 |
| commit | f7b8fb2b34e0453e74ef784947333b7aca56b43b (patch) | |
| tree | 69193bcda9a19ee6090f464aa2223270e49b2543 /biology | |
| parent | 8e6824b7d54f091a577437055b04707b8a38db96 (diff) | |
| download | freebsd-ports-gnome-f7b8fb2b34e0453e74ef784947333b7aca56b43b.tar.gz freebsd-ports-gnome-f7b8fb2b34e0453e74ef784947333b7aca56b43b.tar.zst freebsd-ports-gnome-f7b8fb2b34e0453e74ef784947333b7aca56b43b.zip | |
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>
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/py-pysam/Makefile | 22 | ||||
| -rw-r--r-- | biology/py-pysam/distinfo | 3 | ||||
| -rw-r--r-- | biology/py-pysam/files/patch-setup.py | 11 | ||||
| -rw-r--r-- | biology/py-pysam/pkg-descr | 10 |
5 files changed, 47 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 4818fd772763..85155f710443 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -83,6 +83,7 @@ SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython + SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus diff --git a/biology/py-pysam/Makefile b/biology/py-pysam/Makefile new file mode 100644 index 000000000000..4ed2c427ff1d --- /dev/null +++ b/biology/py-pysam/Makefile @@ -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> diff --git a/biology/py-pysam/distinfo b/biology/py-pysam/distinfo new file mode 100644 index 000000000000..8386380d3fdb --- /dev/null +++ b/biology/py-pysam/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1492580723 +SHA256 (pysam-0.11.tar.gz) = 815c8a6150c5fe21df227e730dd57e4212984ae568854fcc5873e243072dcbad +SIZE (pysam-0.11.tar.gz) = 2425484 diff --git a/biology/py-pysam/files/patch-setup.py b/biology/py-pysam/files/patch-setup.py new file mode 100644 index 000000000000..d82a8bbbefcf --- /dev/null +++ b/biology/py-pysam/files/patch-setup.py @@ -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") + diff --git a/biology/py-pysam/pkg-descr b/biology/py-pysam/pkg-descr new file mode 100644 index 000000000000..3278584b89c1 --- /dev/null +++ b/biology/py-pysam/pkg-descr @@ -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 |