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Port details
py-pysam Python module for reading, manipulating and writing genomic data sets
0.22.0 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 0.22.0Version 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: 2023-12-03 11:51:05
Commit Hash: aefceb7
Also Listed In: python
License: MIT
WWW:
https://github.com/pysam-developers/pysam
Description:
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
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 py39-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 py39-pysam listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-pysam
Package flavors (<flavor>: <package>)
  • py39: py39-pysam
distinfo:
TIMESTAMP = 1696579895 SHA256 (pysam-0.22.0.tar.gz) = ab7a46973cf0ab8c6ac327f4c3fb67698d7ccbeef8631a716898c6ba01ef3e45 SIZE (pysam-0.22.0.tar.gz) = 4631254
Packages (timestamps in pop-ups are UTC):
py37-pysam
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--0.16.0.1---0.16.0.1-
FreeBSD:13:quarterly--------
FreeBSD:14:latest--------
FreeBSD:14:quarterly--------
FreeBSD:15:latest--n/a-n/a---
FreeBSD:15:quarterly--n/a-n/a---
 

py39-pysam
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.22.00.22.0-0.22.00.22.0---
FreeBSD:13:quarterly0.22.00.22.00.21.00.22.00.22.00.22.00.22.00.22.0
FreeBSD:14:latest0.22.00.22.00.20.00.22.00.22.00.21.0-0.21.0
FreeBSD:14:quarterly0.22.00.22.0-0.22.00.22.00.22.00.22.00.22.0
FreeBSD:15:latest0.22.00.22.0n/a0.22.0n/a0.22.00.22.00.22.0
FreeBSD:15:quarterly--n/a-n/a---
 

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-3.9 : lang/cython@py39
  3. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  4. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. cython-3.9 : lang/cython@py39
  2. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  3. python3.9 : lang/python39
Library dependencies:
  1. libhts.so : biology/htslib
This port is required by:
for Build
  1. biology/py-htseq
for Run
  1. biology/biostar-tools
  2. biology/checkm
  3. biology/py-crossmap
  4. biology/py-deeptools
  5. biology/py-htseq
Configuration Options:
No options to configure
Options name:
biology_py-pysam
USES:
gmake python
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: 37

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.22.0
03 Dec 2023 11:51:05
commit hash: aefceb7b596e0acff92461e55c0f0fbbe6751a19commit hash: aefceb7b596e0acff92461e55c0f0fbbe6751a19commit hash: aefceb7b596e0acff92461e55c0f0fbbe6751a19commit hash: aefceb7b596e0acff92461e55c0f0fbbe6751a19 files touched by this commit		 Ruslan Makhmatkhanov (rm) search for other commits by this committer 
biology/py-pysam: relax python version requirement

According to [1] pysam support Python 3.11 since version 0.21.0

[1] https://github.com/pysam-developers/pysam/releases/tag/v0.21.0

PR:		275494
Approved by:	portmgr (blanket)
0.22.0
06 Oct 2023 10:09:08
commit hash: 45df85715f51ac1f90936f774b73002361d9f9bfcommit hash: 45df85715f51ac1f90936f774b73002361d9f9bfcommit hash: 45df85715f51ac1f90936f774b73002361d9f9bfcommit hash: 45df85715f51ac1f90936f774b73002361d9f9bf files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/py-pysam: update 0.21.0 → 0.22.0

Reported by:	portscout
0.21.0
27 Jun 2023 19:34:34
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb files touched by this commit		 Rene Ladan (rene) search for other commits by this committer 
all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>
0.21.0
16 Jun 2023 21:46:56
commit hash: 67a73369637d458cba308db925af904f4964633acommit hash: 67a73369637d458cba308db925af904f4964633acommit hash: 67a73369637d458cba308db925af904f4964633acommit hash: 67a73369637d458cba308db925af904f4964633a files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/py-pysam: Update 0.20.0 → 0.21.0

Reported by:	portscout
0.20.0_1
25 May 2023 09:39:33
commit hash: 41cce74a9e4c1727c4120517724059f68f27404fcommit hash: 41cce74a9e4c1727c4120517724059f68f27404fcommit hash: 41cce74a9e4c1727c4120517724059f68f27404fcommit hash: 41cce74a9e4c1727c4120517724059f68f27404f files touched by this commit		 Robert Clausecker (fuz) search for other commits by this committer 
biology/py-pysam: unbundle biology/htslib

This fixes the build on armv7 by picking up our custom fixed libhts
over the bundled unfixed version.  The CFLAGS workaround is now no
longer required either.

Approved by:	yuri (maintainer)
Differential Revision: https://reviews.freebsd.org/D40251
0.20.0
11 Jan 2023 15:58:34
commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656 files touched by this commit		 Dmitry Marakasov (amdmi3) search for other commits by this committer 
*/*: rename CHEESESHOP to PYPI in MASTER_SITES

PR:			267994
Differential revision:	D37518
Approved by:		bapt
0.20.0
10 Nov 2022 17:36:45
commit hash: db3783aa5833f88f17addb0981560d6af670316ecommit hash: db3783aa5833f88f17addb0981560d6af670316ecommit hash: db3783aa5833f88f17addb0981560d6af670316ecommit hash: db3783aa5833f88f17addb0981560d6af670316e files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/py-pysam: Update 0.19.1 -> 0.20.0

Reported by:	portscout
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
0.19.1_1
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.19.1_1
19 Jul 2022 15:51:56
commit hash: 978fbbf602c743b555117a6c25a836ebfa5bbaf2commit hash: 978fbbf602c743b555117a6c25a836ebfa5bbaf2commit hash: 978fbbf602c743b555117a6c25a836ebfa5bbaf2commit hash: 978fbbf602c743b555117a6c25a836ebfa5bbaf2 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/py-pysam: Remove BROKEN lines
0.19.1_1
19 Jul 2022 15:51:55
commit hash: 8e9198d4043c9022df3502499e3deb1e988d2b9ecommit hash: 8e9198d4043c9022df3502499e3deb1e988d2b9ecommit hash: 8e9198d4043c9022df3502499e3deb1e988d2b9ecommit hash: 8e9198d4043c9022df3502499e3deb1e988d2b9e files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/py-pysam: Fix on aarch64, riscv6 by backporting of symbols failure fix
0.19.1
19 Jul 2022 02:09:00
commit hash: 09d9d827a5c165377dc9e225241b248ea7d145c8commit hash: 09d9d827a5c165377dc9e225241b248ea7d145c8commit hash: 09d9d827a5c165377dc9e225241b248ea7d145c8commit hash: 09d9d827a5c165377dc9e225241b248ea7d145c8 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/py-pysam: Correct BROKEN line; Add comment
0.19.1
15 Jul 2022 02:45:53
commit hash: 2f374bcdfe524d910349e06d52bde62047650b41commit hash: 2f374bcdfe524d910349e06d52bde62047650b41commit hash: 2f374bcdfe524d910349e06d52bde62047650b41commit hash: 2f374bcdfe524d910349e06d52bde62047650b41 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/py-pysam: Broken on arm64 and riscv64

Reported by:	fallout
0.19.1
31 May 2022 00:23:32
commit hash: e8c0b45474cb8504bb2a3b766f55d062771fa2b5commit hash: e8c0b45474cb8504bb2a3b766f55d062771fa2b5commit hash: e8c0b45474cb8504bb2a3b766f55d062771fa2b5commit hash: e8c0b45474cb8504bb2a3b766f55d062771fa2b5 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/py-pysam: Update 0.19.0 -> 0.19.1

Reported by:	portscout
0.19.0
27 Apr 2022 17:38:26
commit hash: 84de6204b99bd08e70929555aa795a4c63e6901bcommit hash: 84de6204b99bd08e70929555aa795a4c63e6901bcommit hash: 84de6204b99bd08e70929555aa795a4c63e6901bcommit hash: 84de6204b99bd08e70929555aa795a4c63e6901b files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/py-pysam: Update 0.18.0 -> 0.19.0

Reported by:	portscout
0.18.0
20 Dec 2021 07:48:52
commit hash: 876147e57df2f60242109ce413ababe3ef14fe51commit hash: 876147e57df2f60242109ce413ababe3ef14fe51commit hash: 876147e57df2f60242109ce413ababe3ef14fe51commit hash: 876147e57df2f60242109ce413ababe3ef14fe51 files touched by this commit		 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
0.16.0.1
01 Nov 2021 13:59:09
commit hash: f9241356e435aa0ca169be46dafaf7748e4b297fcommit hash: f9241356e435aa0ca169be46dafaf7748e4b297fcommit hash: f9241356e435aa0ca169be46dafaf7748e4b297fcommit hash: f9241356e435aa0ca169be46dafaf7748e4b297f files touched by this commit		 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
0.16.0.1
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
0.16.0.1
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
Remove # $FreeBSD$ from Makefiles.
0.16.0.1
28 Dec 2020 23:02:15
Revision:559531Original commit files touched by this commit		 antoine search for other commits by this committer 
Drop python 2.7 support from a few ports

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

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

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

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

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

Reported by:	portscout
0.15.0
30 Jul 2018 19:47:50
Revision:475906Original commit files touched by this commit		 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
0.14.1
25 Apr 2018 16:42:38
Revision:468282Original commit files touched by this commit		 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
0.14.1
21 Mar 2018 08:12:33
Revision:465157Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/py-pysam: Update to 0.14.1

Also silenced STRIP_CMD.

Reported by:	portscout
0.14
10 Feb 2018 23:01:38
Revision:461449Original commit files touched by this commit		 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)
0.13
30 Nov 2017 15:50:34
Revision:455210Original commit files touched by this commit 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)
0.13
05 Nov 2017 19:12:29
Revision:453556Original commit files touched by this commit		 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
0.12.0.1
26 Oct 2017 05:30:35
Revision:452904Original commit files touched by this commit		 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)
0.11.2.2
10 Jun 2017 02:03:39
Revision:443056Original commit files touched by this commit		 wen search for other commits by this committer 
- Update to 0.11.2.2

PR:		219892
Submitted by:	yuri@rawbw.com(maintainer)
0.11.2.1
23 May 2017 22:04:11
Revision:441555Original commit files touched by this commit		 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
0.11.1
07 May 2017 16:06:24
Revision:440347Original commit files touched by this commit		 miwi search for other commits by this committer 
- Update to 0.11.1

PR:		219122
Submitted by:	maintainer
0.11
06 May 2017 06:05:24
Revision:440231Original commit files touched by this commit		 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: 37
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Expired 5
Set to expire 153
Interactive 0
new 24 hours 3
new 48 hours3
new 7 days10
new fortnight53
new month180
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