Perl-bioperl

Introduction

BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/perl-bioperl
Home page: ########################

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

1.7.2-pl526

BELL

1.7.2-pl526

GAUTSCHI

1.7.2-pl526

NEGISHI

1.7.2-pl526

SCHOLAR

1.7.2-pl526

Commands

  • SOAPsh.pl

  • ace.pl

  • bam2bedgraph

  • bamToGBrowse.pl

  • bdf2gdfont.pl

  • bdftogd

  • binhex.pl

  • bp_aacomp.pl

  • bp_biofetch_genbank_proxy.pl

  • bp_bioflat_index.pl

  • bp_biogetseq.pl

  • bp_blast2tree.pl

  • bp_bulk_load_gff.pl

  • bp_chaos_plot.pl

  • bp_classify_hits_kingdom.pl

  • bp_composite_LD.pl

  • bp_das_server.pl

  • bp_dbsplit.pl

  • bp_download_query_genbank.pl

  • bp_extract_feature_seq.pl

  • bp_fast_load_gff.pl

  • bp_fastam9_to_table.pl

  • bp_fetch.pl

  • bp_filter_search.pl

  • bp_find-blast-matches.pl

  • bp_flanks.pl

  • bp_gccalc.pl

  • bp_genbank2gff.pl

  • bp_genbank2gff3.pl

  • bp_generate_histogram.pl

  • bp_heterogeneity_test.pl

  • bp_hivq.pl

  • bp_hmmer_to_table.pl

  • bp_index.pl

  • bp_load_gff.pl

  • bp_local_taxonomydb_query.pl

  • bp_make_mrna_protein.pl

Module

You can load the modules by:

module load biocontainers
module load perl-bioperl

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run perl-bioperl on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=perl-bioperl
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers perl-bioperl

# Your perl-bioperl workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=perl-bioperl
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers perl-bioperl

# Your perl-bioperl workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=perl-bioperl
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers perl-bioperl

# Your perl-bioperl workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=perl-bioperl
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers perl-bioperl

# Your perl-bioperl workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=perl-bioperl
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers perl-bioperl

# Your perl-bioperl workflow...