BSD Portsbiology/barrnap 1.10.6 FreeBSD
BAsic Rapid Ribosomal RNA Predictor
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- GPLv3
- Categories
- biology, science
Description
Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), metazoan mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).
It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new nhmmer tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/barrnap | 1.10.6 |
| DragonFly | biology/barrnap | 0.9 |
| HardenedBSD | biology/barrnap | 1.10.6 |
| GhostBSD | biology/barrnap | 1.10.6 |
Install
Binary package:
pkg install barrnapFrom the ports tree:
cd /usr/ports/biology/barrnap/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= barrnap>0:biology/barrnapPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | - | 1.10.6 | - | 0.9 | - |
| FreeBSD:14:quarterly | - | 1.10.6 | n/a | 0.9 | - |
| FreeBSD:15:latest | - | 1.10.6 | n/a | 0.9 | 0.9 |
| FreeBSD:15:quarterly | - | 1.10.6 | n/a | n/a | n/a |
| FreeBSD:16:latest | - | 1.10.6 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Runtime 6
bedtools: biology/bedtoolscmsearch: biology/infernalp5-File-Which>0: sysutils/p5-File-Whichp5-List-MoreUtils>0: lang/p5-List-MoreUtilsp5-Path-Tiny>0: devel/p5-Path-Tinyseqkit: biology/seqkit
Test 1
bats: devel/bats-core
The full lists below include those, and their dependencies in turn.
Build dependencies 4
Run dependencies 16
No port depends on this one.
Configuration
No options to configure.
- USES
- gmake perl5 shebangfix
- Service scripts
- none
Files
pkg-plist 4
- bin/barrnap
- share/barrnap/db/arc/database.yml
- share/barrnap/db/bac/database.yml
- share/barrnap/db/fun/database.yml
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| tseemann-barrnap-v1.10.6_GH0.tar.gz | 954417 | 6904ca909f59ce8e0952784d59a7d6b5334586f592e1595fa153a917d2a33d62 |
Commit history 0
No commits in the history this site was built from.