Artemis-Teaching

Category

Bioinformatics

Program On

Teaching

Version

17.0.1

Author / Distributor

Artemis

Description

"Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation." More details are at Artemis

Running Program

The last version of this application is at /usr/local/apps/eb/Artemis/17.0.1-Java-1.8.0_144

To use this version, please load the module with

ml Artemis/17.0.1-Java-1.8.0_144 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_Artemis
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=Artemis.%j.out
#SBATCH --error=Artemis.%j.err

cd $SLURM_SUBMIT_DIR
ml Artemis/17.0.1-Java-1.8.0_144
act [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml Artemis/17.0.1-Java-1.8.0_144 
act -h
SYNOPSIS
       Artemis Comparison Tool (ACT): Genome Comparison Tool
USAGE
        /usr/local/apps/eb/Artemis/17.0.1-Java-1.8.0_144/act [options] <SEQUENCE_1> <COMPARISON_1_2> <SEQUENCE_2> ...
OPTIONS
        SEQUENCE                   An EMBL, GenBank, FASTA, or GFF3 file
        FEATURE                    An Artemis TAB file, or GFF file
        COMPARISON                 A BLAST comparison file in tabular format

        -options FILE              Read a text file of options from FILE
        -chado                     Connect to a Chado database (using PGHOST, PGPORT, PGDATABASE, PGUSER environment variables)

        -Dblack_belt_mode=?         Keep warning messages to a minimum [true,false]
        -DuserplotX=FILE[,FILE2]    For sequence 'X' open one or more userplots
        -DloguserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots, take log(data)
        -DbamX=FILE[,FILE2,...]     For sequence 'X' open one or more BAM, CRAM, VCF, or BCF files
        -Dchado="h:p/d?u"           Get ACT to open this CHADO database
        -Dread_only                 Open CHADO database read-only
EXAMPLES
        % act
        % act af063097.embl af063097_v_b132222.crunch b132222.embl
        % act -Dblack_belt_mode=true -Dbam1=MAL_0h.bam -Dbam2=MAL_7h.bam,var.raw.new.bcf
        % act -Duserplot2=/pathToFile/userPlot

HOMEPAGE
        http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

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Installation

Source code is obtained from Artemis

System

64-bit Linux