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
perl [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 
perl -h

Usage: perl [switches] [--] [programfile] [arguments]
  -0[octal]         specify record separator (\0, if no argument)
  -a                autosplit mode with -n or -p (splits $_ into @F)
  -C[number/list]   enables the listed Unicode features
  -c                check syntax only (runs BEGIN and CHECK blocks)
  -d[:debugger]     run program under debugger
  -D[number/list]   set debugging flags (argument is a bit mask or alphabets)
  -e program        one line of program (several -e's allowed, omit programfile)
  -E program        like -e, but enables all optional features
  -f                don't do $sitelib/sitecustomize.pl at startup
  -F/pattern/       split() pattern for -a switch (//'s are optional)
  -i[extension]     edit <> files in place (makes backup if extension supplied)
  -Idirectory       specify @INC/#include directory (several -I's allowed)
  -l[octal]         enable line ending processing, specifies line terminator
  -[mM][-]module    execute "use/no module..." before executing program
  -n                assume "while (<>) { ... }" loop around program
  -p                assume loop like -n but print line also, like sed
  -s                enable rudimentary parsing for switches after programfile
  -S                look for programfile using PATH environment variable
  -t                enable tainting warnings
  -T                enable tainting checks
  -u                dump core after parsing program
  -U                allow unsafe operations
  -v                print version, patchlevel and license
  -V[:variable]     print configuration summary (or a single Config.pm variable)
  -w                enable many useful warnings
  -W                enable all warnings
  -x[directory]     ignore text before #!perl line (optionally cd to directory)
  -X                disable all warnings
  
Run 'perldoc perl' for more help with Perl.

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Installation

Source code is obtained from BioPerl

System

64-bit Linux