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Latest revision as of 10:03, 6 June 2019

This page is will be deleted pending it's creation on the CC wiki.
BIOPERL
Description: Toolkit of perl modules useful in building bioinformatics solutions in Perl
SHARCNET Package information: see BIOPERL software page in web portal
Full list of SHARCNET supported software


Introduction

The BioPerl module provides open source Perl tools for bioinformatics, genomics and life sciences.

Usage on National Platforms (i.e. Graham, Cedar)

BioPerl is installed as a module on cedar and graham:

$ module load bioperl
$ module list
Currently Loaded Modules:
 1) nixpkgs/16.09     (S)      6) intel/2016.4  (t)
 2) imkl/11.3.4.258   (math)   7) openmpi/2.1.1 (m)
 3) icc/.2016.4.258   (H)      8) StdEnv/2016.4 (S)
 4) gcccore/.5.4.0    (H)      9) perl/5.22.4   (t)
 5) ifort/.2016.4.258 (H)     10) bioperl/1.7.1 (bio)


Once the module is loaded one can verify the BioPerl module is usable by doing:

$ perl -e 'use Bio::DB::Taxonomy'

or

$ perl -MBio::DB::Taxonomy -e 1

General Notes

The perl library search paths can be listed by doing:

$ perl -e 'print join("\n", @INC)'
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/perl5/site_perl
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/perl5
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/bioperl/1.7.1/lib/perl5/site_perl/5.22.4/x86_64-linux-thread-multi
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/bioperl/1.7.1/lib/perl5/site_perl/5.22.4
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/bioperl/1.7.1/lib/perl5/site_perl/5.22.4/x86_64-linux-thread-multi
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/bioperl/1.7.1
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/perl5
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/perl5/site_perl
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/perl/5.22.4/lib/perl5/site_perl/5.22.4/x86_64-linux-thread-multi
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/perl/5.22.4/lib/perl5/site_perl/5.22.4
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/perl/5.22.4/lib/perl5/5.22.4/x86_64-linux-thread-multi
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/perl/5.22.4/lib/perl5/5.22.4

Therefore in scripts the following "use lib" line is redundant:

#!/usr/bin/perl
use lib "/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/perl5"; 
use Bio::Perl;

The following stanza shows how a user might customize their ~.bashrc file to find locally installed perl modules. When modifying the PERL5LIB variable be sure to append to it as shown to preserve its settings. When using PERL5OPT its preferred to use "-I/path" instead of "-Mlib=/path" so search paths are inserted before any "-Mload::this::module" settings when using perl on the command line also as shown. For more information see http://perldoc.perl.org/perlrun.html.

export PERL5OPT="-I${HOME}/perl/lib/perl5 -I${HOME}/perl/lib/perl5/site_perl"

and/or

export PERL5LIB=$PERL5LIB:"${HOME}/lib/perl5"

The module also sets up the bin directory into your environment so the following bioperl scripts will be found in your default path:

[/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/bioperl/1.7.1/bin]$ ls
bp_aacomp.pl		      bp_fast_load_gff.pl	bp_local_taxonomydb_query.pl  bp_process_wormbase.pl   bp_seqpart.pl 
bp_biofetch_genbank_proxy.pl  bp_fetch.pl		bp_make_mrna_protein.pl       bp_query_entrez_taxa.pl  bp_seqret.pl
bp_bioflat_index.pl	      bp_filter_search.pl	bp_mask_by_search.pl	      bp_remote_blast.pl       bp_seqretsplit.pl
bp_biogetseq.pl		      bp_find-blast-matches.pl	bp_meta_gff.pl		      bp_revtrans-motif.pl     bp_split_seq.pl
bp_blast2tree.pl	      bp_flanks.pl		bp_mrtrans.pl		      bp_search2alnblocks.pl   bp_sreformat.pl
bp_bulk_load_gff.pl	      bp_gccalc.pl		bp_mutate.pl		      bp_search2gff.pl	       bp_taxid4species.pl
bp_chaos_plot.pl	      bp_genbank2gff3.pl	bp_netinstall.pl	      bp_search2table.pl       bp_taxonomy2tree.pl
bp_classify_hits_kingdom.pl   bp_genbank2gff.pl		bp_nexus2nh.pl		      bp_search2tribe.pl       bp_translate_seq.pl
bp_composite_LD.pl	      bp_generate_histogram.pl	bp_nrdb.pl		      bp_seqconvert.pl	       bp_tree2pag.pl
bp_das_server.pl	      bp_heterogeneity_test.pl	bp_oligo_count.pl	      bp_seqcut.pl	       bp_unflatten_seq.pl
bp_dbsplit.pl		      bp_hivq.pl		bp_pairwise_kaks.pl	      bp_seqfeature_delete.pl
bp_download_query_genbank.pl  bp_hmmer_to_table.pl	bp_parse_hmmsearch.pl	      bp_seqfeature_gff3.pl
bp_extract_feature_seq.pl     bp_index.pl		bp_process_gadfly.pl	      bp_seqfeature_load.pl
bp_fastam9_to_table.pl	      bp_load_gff.pl		bp_process_sgd.pl	      bp_seq_length.pl


Extensive man pages are available as found under directory location:

[/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/bioperl/1.7.1/man]$ ls
man1  man3

For example, to load the bioperl man page do the following:

$ module load bioperl
$ man Bio::Perl

References

o BioPerl Homepage
http://www.bioperl.org/