Purdue University

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

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