| Port details |
- py-pysam Python module for reading, manipulating and writing genomic data sets
- 0.22.1 biology
 =2      0.22.1Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2017-05-06 06:30:42
- Last Update: 2024-04-25 14:52:08
- Commit Hash: c76da4a
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- 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.
  ¦  ¦  ¦  ¦ 
- 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>)
- distinfo:
- TIMESTAMP = 1714015094
SHA256 (pysam-developers-pysam-v0.22.1_GH0.tar.gz) = e4981524d7627c53fa0d3f8cbec2bd65c2ea7520092f25e1029af12cb7b82ff6
SIZE (pysam-developers-pysam-v0.22.1_GH0.tar.gz) = 3885851
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.4.1 : devel/gmake
- cython-3.9 : lang/cython@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- py39-pytest>=7,1 : devel/py-pytest@py39
- python3.9 : lang/python39
- Runtime dependencies:
-
- bcftools : biology/bcftools
- samtools : biology/samtools
- cython-3.9 : lang/cython@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Library dependencies:
-
- libhts.so : biology/htslib
- This port is required by:
- for Build
-
- biology/py-htseq
- for Run
-
- biology/biostar-tools
- biology/checkm
- biology/py-crossmap
- biology/py-deeptools
- 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:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.22.1
25 Apr 2024 14:52:08
 |
Yuri Victorovich (yuri) |
biology/py-pysam: update 0.22.0 → 0.22.1
Reported by: portscout |
0.22.0
03 Dec 2023 11:51:05
|
Ruslan Makhmatkhanov (rm) |
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
|
Yuri Victorovich (yuri) |
biology/py-pysam: update 0.21.0 → 0.22.0
Reported by: portscout |
0.21.0
27 Jun 2023 19:34:34
|
Rene Ladan (rene) |
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
|
Yuri Victorovich (yuri) |
biology/py-pysam: Update 0.20.0 → 0.21.0
Reported by: portscout |
0.20.0_1
25 May 2023 09:39:33
|
Robert Clausecker (fuz) |
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
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
0.20.0
10 Nov 2022 17:36:45
|
Yuri Victorovich (yuri) |
biology/py-pysam: Update 0.19.1 -> 0.20.0
Reported by: portscout |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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
|
Stefan Eßer (se) |
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  ) |
0.19.1_1
19 Jul 2022 15:51:56
|
Yuri Victorovich (yuri) |
biology/py-pysam: Remove BROKEN lines |
0.19.1_1
19 Jul 2022 15:51:55
|
Yuri Victorovich (yuri) |
biology/py-pysam: Fix on aarch64, riscv6 by backporting of symbols failure fix |
0.19.1
19 Jul 2022 02:09:00
|
Yuri Victorovich (yuri) |
biology/py-pysam: Correct BROKEN line; Add comment |
0.19.1
15 Jul 2022 02:45:53
|
Yuri Victorovich (yuri) |
biology/py-pysam: Broken on arm64 and riscv64
Reported by: fallout |
0.19.1
31 May 2022 00:23:32
|
Yuri Victorovich (yuri) |
biology/py-pysam: Update 0.19.0 -> 0.19.1
Reported by: portscout |
0.19.0
27 Apr 2022 17:38:26
|
Yuri Victorovich (yuri) |
biology/py-pysam: Update 0.18.0 -> 0.19.0
Reported by: portscout |
0.18.0
20 Dec 2021 07:48:52
|
Yuri Victorovich (yuri)
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
|
Dmitry Marakasov (amdmi3) |
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
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.16.0.1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.16.0.1
28 Dec 2020 23:02:15
 |
antoine |
Drop python 2.7 support from a few ports
With hat: portmgr |
0.16.0.1
15 Nov 2020 19:26:37
|
yuri |
biology/py-pysam: Update 0.16.0 -> 0.16.0.1 |
0.16.0
09 Jun 2020 05:03:48
|
yuri |
biology/py-pysam: Update 0.15.4 -> 0.16.0
Reported by: potscout |
0.15.4
23 Jan 2020 02:53:10
|
yuri |
biology/py-pysam: Update 0.15.3 -> 0.15.4
Reported by: portscout |
0.15.3
31 Aug 2019 15:49:19
|
yuri |
biology/py-pysam: Update 0.15.2 -> 0.15.3
Reported by: portscout |
0.15.2
26 Jan 2019 04:15:54
|
yuri |
biology/py-pysam: Update 0.15.1 -> 0.15.2
Reported by: portscout |
0.15.1
17 Sep 2018 17:40:28
|
yuri |
biology/py-pysam: Update 0.15.0 -> 0.15.1
Reported by: portscout |
0.15.0
30 Jul 2018 19:47:50
|
yuri |
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
|
amdmi3 |
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
|
yuri |
biology/py-pysam: Update to 0.14.1
Also silenced STRIP_CMD.
Reported by: portscout |
0.14
10 Feb 2018 23:01:38
|
yuri |
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
 |
mat |
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 ) |
0.13
05 Nov 2017 19:12:29
|
yuri |
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
|
tcberner |
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
|
wen |
- Update to 0.11.2.2
PR: 219892
Submitted by: yuri@rawbw.com(maintainer) |
0.11.2.1
23 May 2017 22:04:11
|
joneum |
- 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
|
miwi |
- Update to 0.11.1
PR: 219122
Submitted by: maintainer |
0.11
06 May 2017 06:05:24
|
miwi |
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> |
As an Amazon Associate I earn from qualifying purchases.