Prokka wrapper
==============

Warning
-------

Prokka includes custom databases and is thus about a 2.0 GB download!

Dependencies of Prokka which needs to be installed separately
-------------------------------------------------------------

- Perl core modules: File\::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
- Perl modules: Bio::SeqIO from BioPerl_ >= 1.6.900, `XML::Simple`_;
- tbl2asn_ >= 21.0 is required. This dependency is not managed here since versions are increasing very rapidly;
- SignalP_ >= 3.0 is an optional dependency to find signal peptides. For licensing reasons, it is not used in the tool wrapper.

.. _BioPerl: http://search.cpan.org/dist/BioPerl/
.. _XML::Simple: http://search.cpan.org/dist/XML-Simple/
.. _tbl2asn: http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/
.. _SignalP: http://www.cbs.dtu.dk/services/SignalP/

Configuration
-------------

If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of threads allocated by the job runner according to the configuration of the job destination selected for this tool (see http://wiki.galaxyproject.org/Admin/Config/Jobs ).

If instead you are using an older Galaxy release, you should add a line

  GALAXY_SLOTS=N; export GALAXY_SLOTS

(where N is the number of threads allocated by the job runner) to the file

  <tool_dependencies_dir>/prokka/1.7/crs4/prokka/<hash_string>/env.sh

Version history
---------------

- Release 3 (prokka 1.2.0): Use $GALAXY_SLOTS instead of $PROKKA_SITE_OPTIONS. Upgrade Barrnap dependency to v. 0.3. Upgrade Infernal dependency to v. 1.1. Depend on package_gnu_parallel_20131122 (requires Galaxy release_2013.11.04 or later).
- Release 2 (prokka 1.1.0): Merge the wrappers by CRS4 and Lionel Guy. Directly call prokka, remove prokka.py . Add 'locustag', 'increment', 'gffver', 'compliant', 'addgenes', 'genus', 'species', 'strain', 'plasmid', 'gcode', 'usegenus', 'metagenome', 'fast', 'evalue', 'norrna', 'notrna' params. Upgrade BLAST+ dependency to v. 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
- Release 1 (prokka 1.0.1): Add txt output file. Use a definition list instead of a block quote in <help>. Correct 2 dependency minimum versions.
- Release 0 (prokka 1.0.0): Initial release in the Tool Shed.

Version history of (now deprecated) Lionel Guy's wrapper:

- prokka 1.1.0: Merge the wrappers by CRS4 and Lionel Guy. Add COPYING file with MIT license. Make all params optional. Add 'gffver' param. Correctly quote text params in command. Use float type for 'evalue' param. Describe output files in help. Upgrade BLAST+ dependency to v. 2.2.28. Depend on package_aragorn_1_2_36 instead of trna_prediction. Depend on package_prodigal_2_60 instead of prodigal. Depend on package_barrnap_0_2 instead of barrnap. Add PROKKA_SITE_OPTIONS to env.sh and remove 'cpus' param.
- prokka 0.2: Added this readme file. Support Prokka 1.7. Add dependencies management.
- prokka 0.1: Initial release in the Tool Shed, supports Prokka 1.6.

Development
-----------

Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!