BSD Ports

biology/trimadap 0.1.4 FreeBSD

Trim adapter sequences from Illumina data using heuristic rules

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
MIT
Categories
biology
Package size
12.2 KiB, 22.7 KiB installed

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.

In the other systems

SystemPortVersion
FreeBSDbiology/trimadap0.1.4
NetBSDwip/trimadap0.1.4
DragonFlybiology/trimadap0.1.4
HardenedBSDbiology/trimadap0.1.4
GhostBSDbiology/trimadap0.1.4

Install

Binary package:

pkg install trimadap

From the ports tree:

cd /usr/ports/biology/trimadap/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	trimadap>0:biology/trimadap

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest0.1.40.1.4-0.1.40.1.4
FreeBSD:14:quarterly0.1.40.1.4n/a0.1.40.1.4
FreeBSD:15:latest0.1.40.1.4n/a0.1.40.1.4
FreeBSD:15:quarterly0.1.40.1.4n/an/an/a
FreeBSD:16:latest0.1.40.1.4n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 1

The full lists below include those, and their dependencies in turn.

Build dependencies 1

No port depends on this one.

Configuration

No options to configure.

USES
localbase
Service scripts
none

Files

distinfo 1
FileSizeSHA256
lh3-trimadap-0.1-4-gec5a764_GH0.tar.gz13268fa842c705028054e13dc5be6aab5feb621b0ac54c2ca5bee3ab9eb9046a55ac4

Commit history 1

DateCommitCreditsLog message
2414383046 Jason W. Bacon Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.