BSD Ports

biology/artemis 18.2.0 FreeBSD

DNA sequence viewer and annotation tool

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
bd40198f6b
License
GPLv3
Categories
biology, java
Package size
100873.0 KiB, 112772.4 KiB installed

Description

Artemis is a DNA sequence viewer and annotation tool that allows visualisation of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, reads EMBL or GENBANK format sequences and feature tables, and can work on sequences of any size.

ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis. It can open two or more sequences (and their annotations/features) together with their comparisons (usually the result of running blastn or tblastx searches).

In the other systems

SystemPortVersion
FreeBSDbiology/artemis18.2.0
NetBSDwip/artemis6nb2
DragonFlybiology/artemis17.0.1.11
HardenedBSDbiology/artemis17.0.1.11_2

Install

Binary package:

pkg install artemis

From the ports tree:

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

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

RUN_DEPENDS=	artemis>0:biology/artemis

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:latest17.0.1.11_218.2.017.0.1.1117.0.1.1118.2.0
FreeBSD:14:quarterly17.0.1.11_217.0.1.11_2n/a17.0.1.1117.0.1.11_2
FreeBSD:15:latest18.2.018.2.0n/a17.0.1.1117.0.1.11
FreeBSD:15:quarterly17.0.1.11_217.0.1.11_2n/an/an/a
FreeBSD:16:latest17.0.1.11_218.2.0n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 1

Runtime 1

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

Build dependencies 55
Run dependencies 54

No port depends on this one.

Configuration

No options to configure.

USES
java shebangfix
Service scripts
none

Files

pkg-plist 49
  • artemis-%%PORTVERSION%%/act
  • artemis-%%PORTVERSION%%/art
  • artemis-%%PORTVERSION%%/bamview
  • artemis-%%PORTVERSION%%/dnaplotter
  • artemis-%%PORTVERSION%%/etc/af063097.embl
  • artemis-%%PORTVERSION%%/etc/af063097.fasta
  • artemis-%%PORTVERSION%%/etc/af063097_v_b132222.crunch
  • artemis-%%PORTVERSION%%/etc/b132222.embl
  • artemis-%%PORTVERSION%%/etc/b132222.fasta
  • artemis-%%PORTVERSION%%/etc/c1215.blastn.crunch
  • artemis-%%PORTVERSION%%/etc/c1215.blastn.tab
  • artemis-%%PORTVERSION%%/etc/c1215.embl
  • artemis-%%PORTVERSION%%/etc/c1215.genbank
  • artemis-%%PORTVERSION%%/etc/c1215.seq
  • artemis-%%PORTVERSION%%/etc/chado_extra.sql
  • artemis-%%PORTVERSION%%/etc/feature_keys
  • artemis-%%PORTVERSION%%/etc/feature_keys_gff
  • artemis-%%PORTVERSION%%/etc/go_associations.pl
  • artemis-%%PORTVERSION%%/etc/key_mapping
  • artemis-%%PORTVERSION%%/etc/log4j.properties
  • artemis-%%PORTVERSION%%/etc/options
  • artemis-%%PORTVERSION%%/etc/pombe.usage
  • artemis-%%PORTVERSION%%/etc/project.properties
  • artemis-%%PORTVERSION%%/etc/qualifier_mapping
  • artemis-%%PORTVERSION%%/etc/qualifier_types
  • artemis-%%PORTVERSION%%/etc/qualifier_types_gff
  • artemis-%%PORTVERSION%%/etc/readmeDNADraw.html
  • artemis-%%PORTVERSION%%/etc/results_to_netscape
  • artemis-%%PORTVERSION%%/etc/run_blastn
  • artemis-%%PORTVERSION%%/etc/run_blastp
  • artemis-%%PORTVERSION%%/etc/run_blastx
  • artemis-%%PORTVERSION%%/etc/run_clustalx
  • artemis-%%PORTVERSION%%/etc/run_hth
  • artemis-%%PORTVERSION%%/etc/run_netblastp
  • artemis-%%PORTVERSION%%/etc/run_pepstats
  • artemis-%%PORTVERSION%%/etc/run_sigcleave
  • artemis-%%PORTVERSION%%/etc/run_tblastn
  • artemis-%%PORTVERSION%%/etc/run_tblastx
  • artemis-%%PORTVERSION%%/etc/setup_blast_dbs.sh
  • artemis-%%PORTVERSION%%/etc/versions
  • artemis-%%PORTVERSION%%/etc/writedb_entry
  • artemis-%%PORTVERSION%%/target/jars/act.jar
  • artemis-%%PORTVERSION%%/target/jars/artemis.jar
  • artemis-%%PORTVERSION%%/target/jars/bamview.jar
  • artemis-%%PORTVERSION%%/target/jars/dnaplotter.jar
  • bin/act
  • bin/art
  • bin/bamview
  • bin/dnaplotter
distinfo 2
FileSizeSHA256
artemis-18.2.0-deps.tar.gz8.022369e+0737e047b35d905ddbc6b8af1f3daa0971d4e4e029ee78341bc4608317d9ed4c85
sanger-pathogens-artemis-v18.2.0_GH0.tar.gz1.8847117e+07842c055f5cce021adbaea4f076b2ea80335ab1e44fbaa34b2ab608df6314a18e

Commit history 1

DateCommitCreditsLog message
bd40198f6b Yuri Victorovich biology/artemis: update 17.0.1-11 → 18.2.0