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Port details
py-pysam Python module for reading, manipulating and writing genomic data sets
0.13 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 06 May 2017 06:30:42
Also Listed In: python
License: MIT
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
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (3 items)
  1. /usr/local/share/licenses/py27-pysam-0.13/catalog.mk
  2. /usr/local/share/licenses/py27-pysam-0.13/LICENSE
  3. /usr/local/share/licenses/py27-pysam-0.13/MIT
  4. Collapse this list.

To install the port: cd /usr/ports/biology/py-pysam/ && make install clean
To add the package: pkg install py27-pysam

PKGNAME: py27-pysam

distinfo:

TIMESTAMP = 1509901603
SHA256 (pysam-0.13.tar.gz) = 1829035f58bddf26b0cb6867968178701c2a243518ea697dcedeebff487979af
SIZE (pysam-0.13.tar.gz) = 2586013


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. cython : lang/cython
  2. gmake : devel/gmake
  3. py27-setuptools>0 : devel/py27-setuptools
  4. python2.7 : lang/python27
Runtime dependencies:
  1. cython : lang/cython
  2. py27-setuptools>0 : devel/py27-setuptools
  3. python2.7 : lang/python27
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
gmake python

Master Sites:
  1. https://files.pythonhosted.org/packages/source/p/pysam/
  2. https://pypi.python.org/packages/source/p/pysam/

Number of commits found: 6

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
05 Nov 2017 19:12:29
Original commit files touched by this commit  0.13
Revision:453556
yuri search for other commits by this committer
biology/py-pysam: Update to 0.13

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D12967
26 Oct 2017 05:30:35
Original commit files touched by this commit  0.12.0.1
Revision:452904
tcberner search for other commits by this committer
Update biology/py-pysam to 0.12.0.1

PR:		223254
Submitted by:	Yuri Victorovich <yuri@rawbw.com> (maintainer)
10 Jun 2017 02:03:39
Original commit files touched by this commit  0.11.2.2
Revision:443056
wen search for other commits by this committer
- Update to 0.11.2.2

PR:		219892
Submitted by:	yuri@rawbw.com(maintainer)
23 May 2017 22:04:11
Original commit files touched by this commit  0.11.2.1
Revision:441555
joneum search for other commits by this committer
- Update to 0.11.2.1

PR:	219396
Submitted by:	Yuri Victorovich (Maintainer) <yuri@rawbw.com>
Approved by:	rene (mentor)
Differential Revision:	https://reviews.freebsd.org/D10856
07 May 2017 16:06:24
Original commit files touched by this commit  0.11.1
Revision:440347
miwi search for other commits by this committer
- Update to 0.11.1

PR:		219122
Submitted by:	maintainer
06 May 2017 06:05:24
Original commit files touched by this commit  0.11
Revision:440231
miwi search for other commits by this committer
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>

Number of commits found: 6

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