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Port details
trimadap Trim adapter sequences from Illumina data using heuristic rules
0.1.3_1 biology on this many watch lists=0 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 0.1.3_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-03 18:24:21
Last Update: 2023-08-03 10:40:03
Commit Hash: 1486ac9
License: GPLv2
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.
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
Expand this list (4 items)
Collapse this list.
  1. bin/trimadap-mt
  2. /usr/local/share/licenses/trimadap-0.1.3_1/catalog.mk
  3. /usr/local/share/licenses/trimadap-0.1.3_1/LICENSE
  4. /usr/local/share/licenses/trimadap-0.1.3_1/GPLv2
Collapse this list.
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.
ONLY_FOR_ARCHS: amd64 i386 powerpc64le
distinfo:
TIMESTAMP = 1522773176 SHA256 (lh3-trimadap-0.1-3-gddfef21_GH0.tar.gz) = c2c42a3257d37b12be3523ed0d4415bddd401d72b99b05ba4ae33afaa3c3f373 SIZE (lh3-trimadap-0.1-3-gddfef21_GH0.tar.gz) = 13138

Packages (timestamps in pop-ups are UTC):
trimadap
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-0.1.3_1--0.1.3_1---
FreeBSD:13:quarterly-0.1.3_1--0.1.3_1--0.1.3_1
FreeBSD:14:latest-0.1.3_1--0.1.3_1---
FreeBSD:14:quarterly-0.1.3_1--0.1.3_1--0.1.3_1
FreeBSD:15:latest-0.1.3_1n/a-n/a--0.1.3_1
FreeBSD:15:quarterly--n/a-n/a---
This port has no dependencies.
This port is required by:
for Run
  1. biology/ddocent

Configuration Options:
No options to configure
Options name:
biology_trimadap
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/lh3/trimadap/tar.gz/0.1-3-gddfef21?dummy=/
Collapse this list.

Number of commits found: 10

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.1.3_1
03 Aug 2023 10:40:03
commit hash: 1486ac92464205c5d73778e57ef6b0793314cf60commit hash: 1486ac92464205c5d73778e57ef6b0793314cf60commit hash: 1486ac92464205c5d73778e57ef6b0793314cf60commit hash: 1486ac92464205c5d73778e57ef6b0793314cf60 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/trimadap: drop GCC requirement on powerpc64le

Not necessary on 13.2-RELEASE and up.
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)
0.1.3
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)
0.1.3
25 Oct 2021 12:58:29
commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8commit hash: 61b661339366b6ee95ca1de0667979da9240c6b8 files touched by this commit
Alexey Dokuchaev (danfe) search for other commits by this committer
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
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
0.1.3
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.
0.1.3
06 Apr 2021 09:53:56
commit hash: 5b92ed01d91a2fa9932769a56436c597770ae839commit hash: 5b92ed01d91a2fa9932769a56436c597770ae839commit hash: 5b92ed01d91a2fa9932769a56436c597770ae839commit hash: 5b92ed01d91a2fa9932769a56436c597770ae839 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/trimadap: fix build on powerpc64le

Requires GCC for its SSE translation.
0.1.3
11 May 2019 00:18:24
Revision:501207Original commit files touched by this commit
jwb search for other commits by this committer
biology/trimadap: Mark only for amd64 and i386

Contains hard-coded SSE instructions
0.1.3
21 Jun 2018 23:52:37
Revision:473009Original commit files touched by this commit
linimon search for other commits by this committer
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
Revision:466367Original commit files touched by this commit
jwb search for other commits by this committer
biology/trimadap: Trim adapter sequences from Illumina data

Reviewed by:    mat
Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D14935

Number of commits found: 10