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Port details
py-cutadapt Trim adapters from high-throughput sequencing reads
4.9 biology on this many watch lists=2 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 4.9Version of this port present on the latest quarterly branch.
Maintainer: jadawin@FreeBSD.org search for ports maintained by this maintainer
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.
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:
  • ${PYTHON_PKGNAMEPREFIX}cutadapt>0:biology/py-cutadapt@${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>)
  • py311: py311-cutadapt
distinfo:
TIMESTAMP = 1718872674 SHA256 (cutadapt-4.9.tar.gz) = da3b45775b07334d2e2580a7b154d19ea7e872f0da813bb1ac2a4da712bfc223 SIZE (cutadapt-4.9.tar.gz) = 248837

Packages (timestamps in pop-ups are UTC):
py37-cutadapt
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--2.7---2.7-
FreeBSD:13:quarterly--------
FreeBSD:14:latest--------
FreeBSD:14:quarterly--------
FreeBSD:15:latest--n/a-n/a---
 
py39-cutadapt
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--------
FreeBSD:13:quarterly--3.3_1--3.3_13.3_13.3_1
FreeBSD:14:latest--3.3_1--3.3_1-3.3_1
FreeBSD:14:quarterly-----3.3_13.3_13.3_1
FreeBSD:15:latest--n/a-n/a3.3_13.3_14.6
 
py311-cutadapt
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest4.94.9-4.94.9---
FreeBSD:13:quarterly4.94.9-4.94.9---
FreeBSD:14:latest4.94.9-4.94.9---
FreeBSD:14:quarterly4.94.9-4.94.9---
FreeBSD:15:latest4.94.9n/a4.9n/a---
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py311-setuptools-scm>0 : devel/py-setuptools-scm@py311
  2. cython-3.11 : lang/cython@py311
  3. py311-setuptools>=63.1.0 : devel/py-setuptools@py311
  4. python3.11 : lang/python311
Test dependencies:
  1. py311-pytest>0 : devel/py-pytest@py311
  2. py311-pytest-timeout>0 : devel/py-pytest-timeout@py311
  3. py311-pytest-mock>0 : devel/py-pytest-mock@py311
  4. python3.11 : lang/python311
Runtime dependencies:
  1. py311-xopen>=1.6.0 : archivers/py-xopen@py311
  2. py311-dnaio>=1.2.0 : biology/py-dnaio@py311
  3. py311-setuptools>=63.1.0 : devel/py-setuptools@py311
  4. python3.11 : lang/python311
This port is required by:
for Run
  1. biology/biostar-tools
  2. 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:
Expand this list (2 items)
Collapse this list.
  1. https://files.pythonhosted.org/packages/source/c/cutadapt/
  2. https://pypi.org/packages/source/c/cutadapt/
Collapse this list.

Number of commits found: 31

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
4.9
20 Jun 2024 08:38:00
commit hash: 62058b84ea1651cad66148356f3b8b833880afd6commit hash: 62058b84ea1651cad66148356f3b8b833880afd6commit hash: 62058b84ea1651cad66148356f3b8b833880afd6commit hash: 62058b84ea1651cad66148356f3b8b833880afd6 files touched by this commit
Philippe Audeoud (jadawin) search for other commits by this committer
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
commit hash: 81c4dbffdc146c0f0900669e5978075d7951fdcccommit hash: 81c4dbffdc146c0f0900669e5978075d7951fdcccommit hash: 81c4dbffdc146c0f0900669e5978075d7951fdcccommit hash: 81c4dbffdc146c0f0900669e5978075d7951fdcc files touched by this commit
Philippe Audeoud (jadawin) search for other commits by this committer
biology/py-cutadapt: update to 4.8

While here, take maintainership
4.7
06 Apr 2024 00:12:16
commit hash: 7045d13e4cdf834cac4b89cdeb2640ddb8b470b1commit hash: 7045d13e4cdf834cac4b89cdeb2640ddb8b470b1commit hash: 7045d13e4cdf834cac4b89cdeb2640ddb8b470b1commit hash: 7045d13e4cdf834cac4b89cdeb2640ddb8b470b1 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/py-cutadapt: Release to ports@

Focusing on fastq-trim from now on
4.7
16 Mar 2024 13:31:06
commit hash: 43e4ca8d053f7d8bbcbe62b31dc55f5ce93b782ecommit hash: 43e4ca8d053f7d8bbcbe62b31dc55f5ce93b782ecommit hash: 43e4ca8d053f7d8bbcbe62b31dc55f5ce93b782ecommit hash: 43e4ca8d053f7d8bbcbe62b31dc55f5ce93b782e files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454 files touched by this commit
Charlie Li (vishwin) search for other commits by this committer
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
commit hash: 7c280eb4247df10ec0bebfbe6ffd6d42f36142fbcommit hash: 7c280eb4247df10ec0bebfbe6ffd6d42f36142fbcommit hash: 7c280eb4247df10ec0bebfbe6ffd6d42f36142fbcommit hash: 7c280eb4247df10ec0bebfbe6ffd6d42f36142fb files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
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>
3.3_1
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
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)
3.3_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)
3.3_1
07 Apr 2022 18:59:32
commit hash: ff5a2c36cc59b71af50c6e591cad90426bd8d955commit hash: ff5a2c36cc59b71af50c6e591cad90426bd8d955commit hash: ff5a2c36cc59b71af50c6e591cad90426bd8d955commit hash: ff5a2c36cc59b71af50c6e591cad90426bd8d955 files touched by this commit
Dmitry Marakasov (amdmi3) search for other commits by this committer
biology/py-cutadapt: fix tests by adding missing test depend

Approved by:	portmgr blanket
3.3_1
04 May 2021 13:20:39
commit hash: ba4a5525a202e3f8bbbd5bf1c8881a798963b5d0commit hash: ba4a5525a202e3f8bbbd5bf1c8881a798963b5d0commit hash: ba4a5525a202e3f8bbbd5bf1c8881a798963b5d0commit hash: ba4a5525a202e3f8bbbd5bf1c8881a798963b5d0 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/py-cutadapt: Update strict py-dnaio dep version
3.3
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
3.3
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.
3.3
06 Mar 2021 21:18:15
Revision:567519Original commit files touched by this commit
antoine search for other commits by this committer
Unbreak INDEX
3.3
06 Mar 2021 17:55:38
Revision:567503Original commit files touched by this commit Sanity Test Failure
jwb search for other commits by this committer
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
Revision:563844Original commit files touched by this commit
jwb search for other commits by this committer
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
Revision:518242Original commit files touched by this commit
jwb search for other commits by this committer
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
Revision:511957Original commit files touched by this commit
jwb search for other commits by this committer
biology/py-cutadapt: Upgrade to 2.5

Add pigz run depend for parallel gzip/gunzip
2.3
27 Apr 2019 01:26:17
Revision:500187Original commit files touched by this commit
jwb search for other commits by this committer
biology/py-cutadapt: Upgrade to 2.3

Numerous bugfixes and enhancements since 2.1
2.1_1
10 Apr 2019 06:18:32
Revision:498530Original commit files touched by this commit
antoine search for other commits by this committer
Bump a few PORTREVISIONs after r498529

With hat:	portmgr
2.1
24 Mar 2019 21:20:24
Revision:496783Original commit files touched by this commit
jwb search for other commits by this committer
biology/py-cutadapt: Upgrade to 2.1

Add do-test target
1.18
24 Mar 2019 20:28:55
Revision:496776Original commit files touched by this commit
antoine search for other commits by this committer
Unbreak
1.18
20 Sep 2018 14:10:52
Revision:480173Original commit files touched by this commit
jwb search for other commits by this committer
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
Revision:472884Original commit files touched by this commit
mat search for other commits by this committer
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
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
1.14
08 Feb 2018 20:18:09
Revision:461265Original commit files touched by this commit
amdmi3 search for other commits by this committer
Canonicalize PyPi WWWs:
- Switch to https://
- Remove trailing slashes

Approved by:	portmgr blanket
1.14
01 Dec 2017 06:18:17
Revision:455247Original commit files touched by this commit Sanity Test Failure
antoine search for other commits by this committer
Fix packaging with python3
1.14
30 Nov 2017 22:11:04
Revision:455235Original commit files touched by this commit Sanity Test Failure
jwb search for other commits by this committer
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
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)
1.14
29 Nov 2017 22:17:44
Revision:455154Original commit files touched by this commit
jwb search for other commits by this committer
[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

Number of commits found: 31