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=Introduction=
 
=Introduction=

Revision as of 14:08, 17 July 2017

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


Note: Some of the information on this page is for our legacy systems only. The page is scheduled for an update to make it applicable to Graham.


Introduction

THe sharcnet bioperl module provides BioPerl Perl Modules for Biology built (as of this writting) from the source file BioPerl-1.6.923.tar.gz found here http://search.cpan.org/~cjfields/BioPerl-1.6.923/BioPerl.pm The BioPerl installation directory structure on sharcnet is organized as follows:

[roberpj@mon241:/opt/sharcnet/bioperl/1.6.923] ls
bin  doc  examples  ide  lib  maintenance  man  models  perl  scripts  t

where:

- lib/perl5/Bio/ - BioPerl modules       
- scripts/ - Useful production-quality scripts with POD documentation
- doc/ - Documentation utilities
- examples/ - Scripts demonstrating the many uses of BioPerl
- ide/ - files for developing BioPerl using an IDE
- maintenance/ - BioPerl housekeeping scripts
- models/ - DIA drawing program generated OO UML for BioPerl classes (these are quite out-of-date)
- t/ - Perl built-in tests, tests are divided into subdirectories based on the specific classes being tested
- t/data/ - Data files used for the tests, provides good example data

Version Selection

[roberpj@mon241:~] module load bioperl

Job Submission

coming soon ...

Example Job

coming soon ...

General Notes

Once the sharcnet module is loaded one can verify the bioperl perl module is usable by doing:

[roberpj@mon241:~] perl -e 'use Bio::DB::Taxonomy'
[roberpj@mon241:~]
or
[roberpj@mon241:~] perl -MBio::DB::Taxonomy -e 1
[roberpj@mon241:~] 

The perl library search paths can be listed by doing:

[roberpj@mon241:~] perl -e 'print join("\n", @INC)'
/opt/sharcnet/bioperl/1.6.923/lib/perl5/x86_64-linux-thread-multi
/opt/sharcnet/bioperl/1.6.923/lib/perl5
/opt/sharcnet/bioperl/1.6.923/perl/lib/perl5/x86_64-linux-thread-multi
/opt/sharcnet/bioperl/1.6.923/perl/lib/perl5
/usr/local/lib64/perl5
/usr/local/share/perl5
/usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl
/usr/lib64/perl5
/usr/share/perl5

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

#!/usr/bin/perl
use lib "/opt/sharcnet/bioperl/1.6.923/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 sharcnet module also sets up the bin directory into your environment so the following bioperl scripts will be found in your default path:

[roberpj@mon241:/opt/sharcnet/bioperl/1.6.923/bin] ls
bp_aacomp.pl                  bp_heterogeneity_test.pl      bp_revtrans-motif.pl
bp_biofetch_genbank_proxy.pl  bp_hivq.pl                    bp_search2alnblocks.pl
bp_bioflat_index.pl           bp_hmmer_to_table.pl          bp_search2BSML.pl
bp_biogetseq.pl               bp_index.pl                   bp_search2gff.pl
bp_blast2tree.pl              bp_load_gff.pl                bp_search2table.pl
bp_bulk_load_gff.pl           bp_local_taxonomydb_query.pl  bp_search2tribe.pl
bp_chaos_plot.pl              bp_make_mrna_protein.pl       bp_seqconvert.pl
bp_classify_hits_kingdom.pl   bp_mask_by_search.pl          bp_seqcut.pl
bp_composite_LD.pl            bp_meta_gff.pl                bp_seqfeature_delete.pl
bp_das_server.pl              bp_mrtrans.pl                 bp_seqfeature_gff3.pl
bp_dbsplit.pl                 bp_mutate.pl                  bp_seqfeature_load.pl
bp_download_query_genbank.pl  bp_netinstall.pl              bp_seq_length.pl
bp_extract_feature_seq.pl     bp_nexus2nh.pl                bp_seqpart.pl
bp_fastam9_to_table.pl        bp_nrdb.pl                    bp_seqret.pl
bp_fast_load_gff.pl           bp_oligo_count.pl             bp_seqretsplit.pl
bp_fetch.pl                   bp_pairwise_kaks.pl           bp_split_seq.pl
bp_filter_search.pl           bp_parse_hmmsearch.pl         bp_sreformat.pl
bp_flanks.pl                  bp_process_gadfly.pl          bp_taxid4species.pl
bp_gccalc.pl                  bp_process_sgd.pl             bp_taxonomy2tree.pl
bp_genbank2gff3.pl            bp_process_wormbase.pl        bp_translate_seq.pl
bp_genbank2gff.pl             bp_query_entrez_taxa.pl       bp_tree2pag.pl
bp_generate_histogram.pl      bp_remote_blast.pl            bp_unflatten_seq.pl

Extensive man pages are available as found under directory location:

[roberpj@mon241:/opt/sharcnet/bioperl/1.6.923/man] ls
man1  man3

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

[roberpj@mon241:~] module load bioperl
[roberpj@mon241:~] man Bio::Perl

References

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

o BioPerl Wiki
http://www.bioperl.org/wiki/