BIOPERL |
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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 |
Contents
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- BioPerl housekeeping scripts - models/ - DIA drawing program generated OO UML for BioPerl classes (these are quite out-of-date) - t/ - Perl built-in tests, tests are divided into subdirectories based on the specific classes being tested - t/data/ - Data files used for the tests,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/