| Port details |
- py-dnaio Read and write FASTQ and FASTA
- 1.2.1 biology
 =2      1.2.0Version of this port present on the latest quarterly branch. - Maintainer: wen@FreeBSD.org
- Port Added: 2019-03-24 19:40:53
- Last Update: 2024-07-04 09:15:39
- Commit Hash: b6abf92
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: python
- License: MIT
- WWW:
- https://pypi.python.org/pypi/dnaio
- Description:
- dnaio is a Python 3 library for fast input and output of FASTQ and FASTA files.
It supports paired-end data in separate files, interleaved paired-end in a
single file and compression using gzip, bzip, and xz.
  ¦  ¦  ¦  ¦ 
- 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:
-
- ${PYTHON_PKGNAMEPREFIX}dnaio>0:biology/py-dnaio@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-dnaio/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-dnaio
- pkg install py311-dnaio
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 py311-dnaio listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py311-dnaio
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1720074321
SHA256 (dnaio-1.2.1.tar.gz) = 4786dc63614b9f3011463d9ea9d981723dd38d1091a415a557f71d8c74400f38
SIZE (dnaio-1.2.1.tar.gz) = 59274
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:
-
- py311-setuptools>0 : devel/py-setuptools@py311
- py311-setuptools-scm>0 : devel/py-setuptools-scm@py311
- py311-wheel>=0 : devel/py-wheel@py311
- cython-3.11 : lang/cython@py311
- python3.11 : lang/python311
- py311-build>=0 : devel/py-build@py311
- py311-installer>=0 : devel/py-installer@py311
- Test dependencies:
-
- python3.11 : lang/python311
- Runtime dependencies:
-
- python3.11 : lang/python311
- This port is required by:
- for Run
-
- biology/py-cutadapt
Configuration Options:- No options to configure
- Options name:
- biology_py-dnaio
- USES:
- 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 |
|---|
1.2.1
04 Jul 2024 09:15:39
 |
Wen Heping (wen) |
biology/py-dnaio: Update to 1.2.1
Take maintainership |
1.2.0
29 Jun 2024 05:02:34
|
Jason E. Hale (jhale) |
*/*: Add ${PY_SETUPTOOLS} to BUILD_DEPENDS
Fix build when setuptools is removed from RUN_DEPENDS in
Mk/Uses/python.mk.
PR: 270510
Approved by: portmgr (blanket) |
1.2.0
10 Apr 2024 23:41:31
|
Jason W. Bacon (jwb) |
biology/py-dnaio: Release to ports@
py-dnaio is only used by py-cutadapt, which has been replaced
by fastq-trim in my toolbox |
1.2.0
29 Feb 2024 07:18:32
|
Charlie Li (vishwin) |
devel/py-setuptools-scm: update to 8.0.4
Directory and PORTNAME changed to match normalised name in release
tarball; consumers updated to match.
Although setuptools itself is specified as a run dependency in the
Python package metadata, it is currently left out here to prevent
environment pollution until at least PR 270510 is committed.
Additionally, this version of setuptools-scm requires setuptools>=61,
which means this version is only meant for USE_PYTHON=pep517 ports
as all USE_PYTHON=distutils ports will switch to devel/py-setuptools58
also after PR 270510. science/py-emmet-core is switched to
devel/py-setuptools_scm7 accordingly, as it specifies setuptools-scm<8.
devel/py-{flit-scm,hatch-vcs} have ${PY_SETUPTOOLS} added to
RUN_DEPENDS to compensate.
Further details: https://wiki.freebsd.org/Python/setuptools
Reported by: yuri
Co-authored by: matthew
Exp-run by: antoine (earlier iteration)
Approved by: yuri (science/py-emmet-core, previous iteration)
PR: 272134
Differential Revision: https://reviews.freebsd.org/D39288 |
1.2.0
06 Feb 2024 12:51:39
|
Jason W. Bacon (jwb) |
biology/py-dnaio: Update to 1.2.0
Numerous bug fixes and enhancements since 0.5.1
Changes: https://github.com/marcelm/dnaio/tags
PR: 276814
Reported by: wen |
0.5.1
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> |
0.5.1
11 Jan 2023 15:58:34
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
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) |
0.5.1
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  ) |
0.5.1
04 May 2021 13:19:25
|
Jason W. Bacon (jwb) |
biology/py-dnaio: Update to 0.5.1
Add py.typed and distribute .pyi files |
0.5.0
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.5.0
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.5.0
02 Feb 2021 20:39:09
 |
jwb |
biology/py-cutadapt: Update to 3.2
biology/py-dnaio: Update to 0.5.0
archivers/py-xopen: Update to 1.0.0
Numerous bug fixes and enhancements since cutadapt 3.2
Document cutadapt dependency versions dnaio~=0.5.0 xopen~=1.0.0
Bump python dependency to 3.6+ to restrict package builds |
0.4.2
24 May 2020 15:23:15
|
jwb |
biology/py-dnaio: Upgrade to 0.4.2
Reported by: portscout |
0.4.1
23 Nov 2019 14:40:00
|
jwb |
biology/py-dnaio: Upgrade to 0.4.1
Needed for py-cutadapt 2.7 |
0.3
24 Mar 2019 19:40:26
|
jwb |
biology/py-dnaio: Read and write FASTQ and FASTA
Factored out of py-cutadapt
Reviewed by: jrm |
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