| Port details |
- trimadap Trim adapter sequences from Illumina data using heuristic rules
- 0.1.4 biology
 =2      0.1.4Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2018-04-03 18:24:21
- Last Update: 2025-01-29 16:56:25
- Commit Hash: c8803c6
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: MIT
- WWW:
- https://github.com/lh3/trimadap
- Description:
- Trimadap is a small tool to trim adapter sequences from Illumina data. It
performs SSE2-SW between each read and each adapter sequence and identifies
adapter sequences with a few heuristic rules which can be found in the
ta_trim1() function in trimadap-mt.c. The default adapters it uses are included
in illumina.txt. These are typical Illumina adapters from paired-end
sequencing.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- trimadap>0:biology/trimadap
- To install the port:
- cd /usr/ports/biology/trimadap/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/trimadap
- pkg install trimadap
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: trimadap
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1729109026
SHA256 (lh3-trimadap-0.1-4-gec5a764_GH0.tar.gz) = fa842c705028054e13dc5be6aab5feb621b0ac54c2ca5bee3ab9eb9046a55ac4
SIZE (lh3-trimadap-0.1-4-gec5a764_GH0.tar.gz) = 13268
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:
-
- simde>0 : devel/simde
- This port is required by:
- for Run
-
- biology/ddocent
Configuration Options:- No options to configure
- Options name:
- biology_trimadap
- USES:
- localbase
- 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 |
|---|
0.1.4
29 Jan 2025 16:56:25
 |
Piotr Kubaj (pkubaj) |
biology/trimadap: drop not necessary powerpc64le knob |
0.1.4
18 Oct 2024 11:37:12
|
Jason W. Bacon (jwb) |
biology/trimadap: Update to 0.1.4
Update to latest commit, with new MIT license
Add support for other architectures using SIMDE
Reported by: fuz
Reviewed by: fuz
Differential Revision: https://reviews.freebsd.org/D47129 |
0.1.3_1
03 Aug 2023 10:40:03
|
Piotr Kubaj (pkubaj) |
biology/trimadap: drop GCC requirement on powerpc64le
Not necessary on 13.2-RELEASE and up. |
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) |
0.1.3
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  ) |
0.1.3
25 Oct 2021 12:58:29
|
Alexey Dokuchaev (danfe) |
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should
start with lower-case letter and not end with a period which is added
by the framework, similar to other knobs like BROKEN, IGNORE, et al.
While here, remove needless quoting, add missing Oxford comma, expand
contractions and jargonisms, use correct spelling for proper names. |
0.1.3
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.1.3
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.1.3
06 Apr 2021 09:53:56
|
Piotr Kubaj (pkubaj) |
biology/trimadap: fix build on powerpc64le
Requires GCC for its SSE translation. |
0.1.3
11 May 2019 00:18:24
 |
jwb |
biology/trimadap: Mark only for amd64 and i386
Contains hard-coded SSE instructions |
0.1.3
21 Jun 2018 23:52:37
|
linimon |
Mark as broken on aarch64, and, where appropriate, armvX.
While here, pet portlint.
Approved by: portmgr (tier-2 blanket) |
0.1.3
03 Apr 2018 18:23:54
|
jwb |
biology/trimadap: Trim adapter sequences from Illumina data
Reviewed by: mat
Approved by: jrm
Differential Revision: https://reviews.freebsd.org/D14935 |
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