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 its website: https://biocontainers.pro/tools/perl-bioperl.

Versions

  • 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

  • bp_mask_by_search.pl

  • bp_meta_gff.pl

  • bp_mrtrans.pl

  • bp_mutate.pl

  • bp_netinstall.pl

  • bp_nexus2nh.pl

  • bp_nrdb.pl

  • bp_oligo_count.pl

  • bp_pairwise_kaks

  • bp_parse_hmmsearch.pl

  • bp_process_gadfly.pl

  • bp_process_sgd.pl

  • bp_process_wormbase.pl

  • bp_query_entrez_taxa.pl

  • bp_remote_blast.pl

  • bp_revtrans-motif.pl

  • bp_search2alnblocks.pl

  • bp_search2gff.pl

  • bp_search2table.pl

  • bp_search2tribe.pl

  • bp_seq_length.pl

  • bp_seqconvert.pl

  • bp_seqcut.pl

  • bp_seqfeature_delete.pl

  • bp_seqfeature_gff3.pl

  • bp_seqfeature_load.pl

  • bp_seqpart.pl

  • bp_seqret.pl

  • bp_seqretsplit.pl

  • bp_split_seq.pl

  • bp_sreformat.pl

  • bp_taxid4species.pl

  • bp_taxonomy2tree.pl

  • bp_translate_seq.pl

  • bp_tree2pag.pl

  • bp_unflatten_seq.pl

  • ccconfig

  • chartex

  • chi2

  • chrom_sizes.pl

  • circo

  • clustalw

  • clustalw2

  • corelist

  • cpan

  • cpanm

  • dbilogstrip

  • dbiprof

  • dbiproxy

  • debinhex.pl

  • enc2xs

  • encguess

  • genomeCoverageBed.pl

  • h2ph

  • h2xs

  • htmltree

  • instmodsh

  • json_pp

  • json_xs

  • lwp-download

  • lwp-dump

  • lwp-mirror

  • lwp-request

  • perl

  • perl5.26.2

  • perlbug

  • perldoc

  • perlivp

  • perlthanks

  • piconv

  • pl2pm

  • pod2html

  • pod2man

  • pod2text

  • pod2usage

  • podchecker

  • podselect

  • prove

  • ptar

  • ptardiff

  • ptargrep

  • shasum

  • splain

  • stag-autoschema.pl

  • stag-db.pl

  • stag-diff.pl

  • stag-drawtree.pl

  • stag-filter.pl

  • stag-findsubtree.pl

  • stag-flatten.pl

  • stag-grep.pl

  • stag-handle.pl

  • stag-itext2simple.pl

  • stag-itext2sxpr.pl

  • stag-itext2xml.pl

  • stag-join.pl

  • stag-merge.pl

  • stag-mogrify.pl

  • stag-parse.pl

  • stag-query.pl

  • stag-splitter.pl

  • stag-view.pl

  • stag-xml2itext.pl

  • stubmaker.pl

  • t_coffee

  • tpage

  • ttree

  • unflatten

  • webtidy

  • xml_grep

  • xml_merge

  • xml_pp

  • xml_spellcheck

  • xml_split

  • xpath

  • xsubpp

  • zipdetails

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 BioPerl on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation 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
ml biocontainers perl-bioperl