Artemis-Teaching: Difference between revisions
(Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 17.0.1 ===...") |
No edit summary |
||
Line 23: | Line 23: | ||
The last version of this application is at /usr/local/apps/eb/Artemis/17.0.1-Java-1.8.0_144 | 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 | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml Artemis/17.0.1-Java-1.8.0_144 | ml Artemis/17.0.1-Java-1.8.0_144 | ||
</pre> | </pre> | ||
Here is an example of a shell script, sub.sh, to run on | Here is an example of a shell script, sub.sh, to run on the batch queue: | ||
<div class="gscript2"> | <div class="gscript2"> |
Revision as of 13:47, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
17.0.1
Author / Distributor
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
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 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
Installation
Source code is obtained from Artemis
System
64-bit Linux