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Port details
py-pysam Python module for reading, manipulating and writing genomic data sets
0.19.0 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 View this port on Repology. pkg-fallout 0.18.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-05-06 06:30:42
Last Update: 2022-04-27 17:38:26
Commit Hash: 84de620
Also Listed In: python
License: MIT
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
There is no configure plist information for this port.
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR}
To install the port:
cd /usr/ports/biology/py-pysam/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/py-pysam
  • pkg install py38-pysam
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.NOTE: This is a Python port. Instead of py38-pysam listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py38-pysam
Package flavors (<flavor>: <package>)
  • py38: py38-pysam
distinfo:
Packages (timestamps in pop-ups are UTC):
py27-pysam
ABIlatestquarterly
FreeBSD:11:aarch640.15.10.16.0
FreeBSD:11:amd64--
FreeBSD:11:armv6-0.16.0
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64-0.16.0
FreeBSD:12:aarch640.15.1-
FreeBSD:12:amd64--
FreeBSD:12:armv60.15.10.16.0
FreeBSD:12:armv70.15.10.16.0
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips640.15.10.16.0
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 
py36-pysam
ABIlatestquarterly
FreeBSD:11:aarch640.15.1-
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch640.15.1-
FreeBSD:12:amd64--
FreeBSD:12:armv60.15.1-
FreeBSD:12:armv70.15.1-
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips640.15.1-
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 
py37-pysam
ABIlatestquarterly
FreeBSD:11:aarch64-0.16.0
FreeBSD:11:amd64--
FreeBSD:11:armv6-0.16.0
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64-0.16.0
FreeBSD:12:aarch64--
FreeBSD:12:amd64--
FreeBSD:12:armv6-0.16.0
FreeBSD:12:armv7-0.16.0
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64-0.16.0
FreeBSD:12:powerpc64-0.16.0.1
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv60.16.0.1-
FreeBSD:13:armv70.16.0.1-
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc640.16.0.1-
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc640.16.0.1-
 
py38-pysam
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd640.16.0.10.16.0.1
FreeBSD:11:armv6--
FreeBSD:11:i3860.16.0.10.16.0.1
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-0.18.0
FreeBSD:12:amd640.19.00.18.0
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3860.19.00.18.0
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64-0.18.0
FreeBSD:13:amd640.19.00.18.0
FreeBSD:13:armv6-0.18.0
FreeBSD:13:armv7-0.18.0
FreeBSD:13:i3860.19.00.18.0
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64-0.16.0.1
FreeBSD:14:aarch64--
FreeBSD:14:amd640.19.0-
FreeBSD:14:armv60.19.0-
FreeBSD:14:armv70.19.0-
FreeBSD:14:i3860.19.0-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. cython-3.8 : lang/cython@py38
  3. py38-setuptools>0 : devel/py-setuptools@py38
  4. python3.8 : lang/python38
Runtime dependencies:
  1. cython-3.8 : lang/cython@py38
  2. py38-setuptools>0 : devel/py-setuptools@py38
  3. python3.8 : lang/python38
This port is required by:
for Run
  1. biology/biostar-tools
  2. biology/checkm
  3. biology/py-crossmap
  4. biology/py-deeptools

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (2 items)
Collapse this list.
  1. https://files.pythonhosted.org/packages/source/p/pysam/
  2. https://pypi.org/packages/source/p/pysam/
Collapse this list.

Number of commits found: 23

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
27 Apr 2022 17:38:26
 files touched by this commit commit hash:84de6204b99bd08e70929555aa795a4c63e6901b  0.19.0
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pysam: Update 0.18.0 -> 0.19.0

Reported by:	portscout
20 Dec 2021 07:48:52
 files touched by this commit commit hash:876147e57df2f60242109ce413ababe3ef14fe51  0.18.0
Yuri Victorovich (yuri) search for other commits by this committer
Author: Wen Heping
biology/py-pysam: Update 0.16.0.1 -> 0.18.0

PR:		260556
01 Nov 2021 13:59:09
 files touched by this commit commit hash:f9241356e435aa0ca169be46dafaf7748e4b297f  0.16.0.1
Dmitry Marakasov (amdmi3) search for other commits by this committer
biology/py-pysam: limit supported python versions

pysam/libchtslib.c:1269:15: error: no member named 'use_tracing' in 'struct _ts'
      tstate->use_tracing = 0;

Approved by:	portmgr blanket
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  0.16.0.1
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  0.16.0.1
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
28 Dec 2020 23:02:15
Original commit files touched by this commit Revision:559531  0.16.0.1
antoine search for other commits by this committer
Drop python 2.7 support from a few ports

With hat:	portmgr
15 Nov 2020 19:26:37
Original commit files touched by this commit Revision:555425  0.16.0.1
yuri search for other commits by this committer
biology/py-pysam: Update 0.16.0 -> 0.16.0.1
09 Jun 2020 05:03:48
Original commit files touched by this commit Revision:538275  0.16.0
yuri search for other commits by this committer
biology/py-pysam: Update 0.15.4 -> 0.16.0

Reported by:	potscout
23 Jan 2020 02:53:10
Original commit files touched by this commit Revision:523862  0.15.4
yuri search for other commits by this committer
biology/py-pysam: Update 0.15.3 -> 0.15.4

Reported by:	portscout
31 Aug 2019 15:49:19
Original commit files touched by this commit Revision:510398  0.15.3
yuri search for other commits by this committer
biology/py-pysam: Update 0.15.2 -> 0.15.3

Reported by:	portscout
26 Jan 2019 04:15:54
Original commit files touched by this commit Revision:491232  0.15.2
yuri search for other commits by this committer
biology/py-pysam: Update 0.15.1 -> 0.15.2

Reported by:	portscout
17 Sep 2018 17:40:28
Original commit files touched by this commit Revision:479938  0.15.1
yuri search for other commits by this committer
biology/py-pysam: Update 0.15.0 -> 0.15.1

Reported by:	portscout
30 Jul 2018 19:47:50
Original commit files touched by this commit Revision:475906  0.15.0
yuri search for other commits by this committer
biology/py-pysam: Update 0.14.1 -> 0.15.0

Port changes:
* Remove stripping: done by the project now
* Update WWW

Reported by:	portscout
25 Apr 2018 16:42:38
Original commit files touched by this commit Revision:468282  0.14.1
amdmi3 search for other commits by this committer
Switch all pypi.python.org WWWs to a new PyPi home pypi.org where
they now redirect to anyway. All new urls checked to return 200,
I've fixed a couple of them in the process.

Approved by:	portmgr blanket, mat
21 Mar 2018 08:12:33
Original commit files touched by this commit Revision:465157  0.14.1
yuri search for other commits by this committer
biology/py-pysam: Update to 0.14.1

Also silenced STRIP_CMD.

Reported by:	portscout
10 Feb 2018 23:01:38
Original commit files touched by this commit Revision:461449  0.14
yuri search for other commits by this committer
biology/py-pysam: Update to 0.14

Changelog:
https://github.com/pysam-developers/pysam/releases/tag/v0.14

Reported by:	portscout
Approved by:	tcberner (mentor, implicit)
30 Nov 2017 15:50:34
Original commit files touched by this commit Revision:455210  0.13  Sanity Test Failure
mat search for other commits by this committer
Convert Python ports to FLAVORS.

  Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
05 Nov 2017 19:12:29
Original commit files touched by this commit Revision:453556  0.13
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 Revision:452904  0.12.0.1
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 Revision:443056  0.11.2.2
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 Revision:441555  0.11.2.1
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 Revision:440347  0.11.1
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 Revision:440231  0.11
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: 23