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{{Software
 
{{Software
 
|package_name=BIOPERL
 
|package_name=BIOPERL
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=Introduction=
 
=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:
+
The BioPerl module provides open source Perl tools for bioinformatics, genomics and life sciences.
  
<source lang="bash">
+
=Usage on National Platforms (i.e. Graham, Cedar)=
[roberpj@mon241:/opt/sharcnet/bioperl/1.6.923] ls
+
bin  doc  examples  ide  lib  maintenance  man  models  perl  scripts  t
+
</source>
+
  
where:
+
BioPerl is installed as a module on cedar and graham:
  
<pre>
+
$ module load bioperl
- lib/perl5/Bio/ - BioPerl modules     
+
$ module list
- scripts/ - Useful production-quality scripts with POD documentation
+
Currently Loaded Modules:
- doc/ - Documentation utilities
+
  1) nixpkgs/16.09    (S)      6) intel/2016.4  (t)
- examples/ - Scripts demonstrating the many uses of BioPerl
+
  2) imkl/11.3.4.258  (math)  7) openmpi/2.1.1 (m)
- ide/ - files for developing BioPerl using an IDE
+
  3) icc/.2016.4.258  (H)     8) StdEnv/2016.4 (S)
- maintenance/ - BioPerl housekeeping scripts
+
  4) gcccore/.5.4.0    (H)      9) perl/5.22.4  (t)
- models/ - DIA drawing program generated OO UML for BioPerl classes (these are quite out-of-date)
+
  5) ifort/.2016.4.258 (H)    10) bioperl/1.7.1 (bio)
- 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
+
</pre>
+
  
=Version Selection=
 
  
<pre>
+
Once the module is loaded one can verify the BioPerl  module is usable by doing:
[roberpj@mon241:~] module load bioperl
+
</pre>
+
  
=Job Submission=
+
$ perl -e 'use Bio::DB::Taxonomy'
  
coming soon ...
+
or
 
+
=Example Job=
+
  
coming soon ...
+
$ perl -MBio::DB::Taxonomy -e 1
  
 
=General Notes=
 
=General Notes=
 
Once the sharcnet module is loaded one can verify the bioperl perl module is usable by doing:
 
 
<pre>
 
[roberpj@mon241:~] perl -e 'use Bio::DB::Taxonomy'
 
[roberpj@mon241:~]
 
or
 
[roberpj@mon241:~] perl -MBio::DB::Taxonomy -e 1
 
[roberpj@mon241:~]
 
</pre>
 
  
 
The perl library search paths can be listed by doing:
 
The perl library search paths can be listed by doing:
  
<source lang="bash">
+
$ perl -e 'print join("\n", @INC)'
[roberpj@mon241:~] perl -e 'print join("\n", @INC)'
+
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/perl5/site_perl
/opt/sharcnet/bioperl/1.6.923/lib/perl5/x86_64-linux-thread-multi
+
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/perl5
/opt/sharcnet/bioperl/1.6.923/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
/opt/sharcnet/bioperl/1.6.923/perl/lib/perl5/x86_64-linux-thread-multi
+
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/bioperl/1.7.1/lib/perl5/site_perl/5.22.4
/opt/sharcnet/bioperl/1.6.923/perl/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
/usr/local/lib64/perl5
+
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/bioperl/1.7.1
/usr/local/share/perl5
+
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/perl5
/usr/lib64/perl5/vendor_perl
+
/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/perl5/site_perl
/usr/share/perl5/vendor_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
/usr/lib64/perl5
+
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/perl/5.22.4/lib/perl5/site_perl/5.22.4
/usr/share/perl5
+
/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/perl/5.22.4/lib/perl5/5.22.4/x86_64-linux-thread-multi
</source>
+
/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:
 
Therefore in scripts the following "use lib" line is redundant:
  
<pre>
+
#!/usr/bin/perl
#!/usr/bin/perl
+
use lib "/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/perl5";  
use lib "/opt/sharcnet/bioperl/1.6.923/lib/perl5";
+
use Bio::Perl;
use Bio::Perl;
+
</pre>
+
  
 
The following stanza shows how a user might customize their <i>~.bashrc</i> 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.
 
The following stanza shows how a user might customize their <i>~.bashrc</i> 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.
  
<source lang="bash">
+
export PERL5OPT="-I${HOME}/perl/lib/perl5 -I${HOME}/perl/lib/perl5/site_perl"
export PERL5OPT="-I${HOME}/perl/lib/perl5 -I${HOME}/perl/lib/perl5/site_perl"
+
 
 
and/or
 
and/or
export PERL5LIB=$PERL5LIB:"${HOME}/lib/perl5"
 
</source>
 
  
The sharcnet module also sets up the bin directory into your environment so the following bioperl scripts will be found in your default path:
+
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
  
<pre>
 
[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
 
</pre>
 
  
 
Extensive man pages are available as found under directory location:
 
Extensive man pages are available as found under directory location:
  
<pre>
+
[/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/bioperl/1.7.1/man]$ ls
[roberpj@mon241:/opt/sharcnet/bioperl/1.6.923/man] ls
+
man1  man3
man1  man3
+
</pre>
+
  
 
For example, to load the <b>bioperl</b> man page do the following:
 
For example, to load the <b>bioperl</b> man page do the following:
  
<pre>
+
$ module load bioperl
[roberpj@mon241:~] module load bioperl
+
$ man Bio::Perl
[roberpj@mon241:~] man Bio::Perl
+
</pre>
+
  
 
=References=
 
=References=
Line 132: Line 97:
 
o BioPerl Homepage<br>
 
o BioPerl Homepage<br>
 
http://www.bioperl.org/
 
http://www.bioperl.org/
 
o BioPerl Wiki<br>
 
http://www.bioperl.org/wiki/
 
  
 
[[Category:Bioinformatics]]
 
[[Category:Bioinformatics]]
  
 
<!--checked2015-->
 
<!--checked2015-->

Latest revision as of 09:03, 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/