perl-bioperl
Link to section 'Introduction' of '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 its website: https://biocontainers.pro/tools/perl-bioperl.
Link to section 'Versions' of 'perl-bioperl' Versions
- 1.7.2-pl526
Link to section 'Commands' of 'perl-bioperl' 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
Link to section 'Module' of 'perl-bioperl' Module
You can load the modules by:
module load biocontainers
module load perl-bioperl
Link to section 'Example job' of '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