Port details |
- py-cutadapt Trim adapters from high-throughput sequencing reads
- 4.9 biology =2 4.9Version of this port present on the latest quarterly branch.
- Maintainer: jadawin@FreeBSD.org
- Port Added: 2017-11-29 22:17:53
- Last Update: 2024-06-20 08:38:00
- Commit Hash: 62058b8
- 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/marcelm/cutadapt/
- Description:
- Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
types of unwanted sequences from your high-throughput sequencing reads.
- ¦ ¦ ¦ ¦
- 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:
-
- ${PYTHON_PKGNAMEPREFIX}cutadapt>0:biology/py-cutadapt@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-cutadapt/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-cutadapt
- pkg install py311-cutadapt
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-cutadapt listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py311-cutadapt
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1718872674
SHA256 (cutadapt-4.9.tar.gz) = da3b45775b07334d2e2580a7b154d19ea7e872f0da813bb1ac2a4da712bfc223
SIZE (cutadapt-4.9.tar.gz) = 248837
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-scm>0 : devel/py-setuptools-scm@py311
- cython-3.11 : lang/cython@py311
- py311-setuptools>=63.1.0 : devel/py-setuptools@py311
- python3.11 : lang/python311
- Test dependencies:
-
- py311-pytest>0 : devel/py-pytest@py311
- py311-pytest-timeout>0 : devel/py-pytest-timeout@py311
- py311-pytest-mock>0 : devel/py-pytest-mock@py311
- python3.11 : lang/python311
- Runtime dependencies:
-
- py311-xopen>=1.6.0 : archivers/py-xopen@py311
- py311-dnaio>=1.2.0 : biology/py-dnaio@py311
- py311-setuptools>=63.1.0 : devel/py-setuptools@py311
- python3.11 : lang/python311
- This port is required by:
- for Run
-
- biology/biostar-tools
- biology/p5-TrimGalore
Configuration Options:
- No options to configure
- Options name:
- biology_py-cutadapt
- 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 |
4.9 20 Jun 2024 08:38:00 |
Philippe Audeoud (jadawin) |
biology/py-cutadapt: update to 4.9
changelog:
https://cutadapt.readthedocs.io/en/stable/changes.html#v4-9-2024-06-19 |
4.8 28 May 2024 11:28:21 |
Philippe Audeoud (jadawin) |
biology/py-cutadapt: update to 4.8
While here, take maintainership |
4.7 06 Apr 2024 00:12:16 |
Jason W. Bacon (jwb) |
biology/py-cutadapt: Release to ports@
Focusing on fastq-trim from now on |
4.7 16 Mar 2024 13:31:06 |
Jason W. Bacon (jwb) |
py-cutadapt: Update to 4.7
Send error message to stderr
Add support for single-ended uBAM
Drop Python 3.7
Changes: https://cutadapt.readthedocs.io/en/stable/changes.html
Reported by: portscout |
4.6 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 |
4.6 06 Feb 2024 12:55:32 |
Jason W. Bacon (jwb) |
biology/py-cutadapt: Update to 4.6
Numerous bug fixes and enhancements since 3.3
Changes: https://github.com/marcelm/cutadapt/tags
PR: 276814
Reported by: wen |
3.3_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> |
3.3_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) |
3.3_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 ) |
3.3_1 07 Apr 2022 18:59:32 |
Dmitry Marakasov (amdmi3) |
biology/py-cutadapt: fix tests by adding missing test depend
Approved by: portmgr blanket |
3.3_1 04 May 2021 13:20:39 |
Jason W. Bacon (jwb) |
biology/py-cutadapt: Update strict py-dnaio dep version |
3.3 07 Apr 2021 08:09:01 |
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
3.3 06 Apr 2021 14:31:07 |
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
3.3 06 Mar 2021 21:18:15 |
antoine |
Unbreak INDEX |
3.3 06 Mar 2021 17:55:38 |
jwb |
py-cutadapt: Update to 3.3
Numerous small bug fixes and enhancements, code refactoring
py-xopen: Update to 1.1.0
Required by cutadapt 3.3
Drop python 3.5 support
Add isal support (not yet utilized in FreeBSD port) |
3.2 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 |
2.7 23 Nov 2019 14:45:53 |
jwb |
biology/py-cutadapt: Upgrade to 2.7
Numerous minor fixes and enhancements.
Upstreamed setup.py patches for dependency versions.
Reported by: portscout |
2.5 13 Sep 2019 13:17:26 |
jwb |
biology/py-cutadapt: Upgrade to 2.5
Add pigz run depend for parallel gzip/gunzip |
2.3 27 Apr 2019 01:26:17 |
jwb |
biology/py-cutadapt: Upgrade to 2.3
Numerous bugfixes and enhancements since 2.1 |
2.1_1 10 Apr 2019 06:18:32 |
antoine |
Bump a few PORTREVISIONs after r498529
With hat: portmgr |
2.1 24 Mar 2019 21:20:24 |
jwb |
biology/py-cutadapt: Upgrade to 2.1
Add do-test target |
1.18 24 Mar 2019 20:28:55 |
antoine |
Unbreak |
1.18 20 Sep 2018 14:10:52 |
jwb |
biology/py-cutadapt: Upgrade to 1.18
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D17099 |
1.14 20 Jun 2018 17:05:44 |
mat |
Use PY_FLAVOR for dependencies.
FLAVOR is the current port's flavor, it should not be used outside of
this scope.
Sponsored by: Absolight |
1.14 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 |
1.14 08 Feb 2018 20:18:09 |
amdmi3 |
Canonicalize PyPi WWWs:
- Switch to https://
- Remove trailing slashes
Approved by: portmgr blanket |
1.14 01 Dec 2017 06:18:17 |
antoine |
Fix packaging with python3 |
1.14 30 Nov 2017 22:11:04 |
jwb |
biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor comment
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D13303 |
1.14 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 ) |
1.14 29 Nov 2017 22:17:44 |
jwb |
[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po
ly-A tails, etc
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D13294 |