BioPerl-Teaching

Category

Bioinformatics

Program On

Teaching

Version

1.7.1

Author / Distributor

BioPerl

Description

"Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects." More details are at BioPerl

Running Program

The last version of this application is at /usr/local/apps/eb/BioPerl/1.7.1-foss-2016b-Perl-5.24.1

To use this version, please load the module with

ml BioPerl/1.7.1-foss-2016b-Perl-5.24.1 

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

#!/bin/bash
#SBATCH --job-name=j_BioPerl
#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=BioPerl.%j.out
#SBATCH --error=BioPerl.%j.err

cd $SLURM_SUBMIT_DIR
ml BioPerl/1.7.1-foss-2016b-Perl-5.24.1

[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 BioPerl/1.7.1-foss-2016b-Perl-5.24.1 
 

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Installation

Source code is obtained from BioPerl

System

64-bit Linux