annotate readme.rst @ 1:2bb7c28ea68f draft

Committed version 0.2: added dependency management and a readme file, and support prokka 1.7

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

Warning
-------

Prokka comes with custom databases and is thus very large: **~2Gb**!

Note
----

- **infernal** >= 1.1rc4 is an optional dependency to find non-coding RNAs. An executable is shipped with prokka.
- **SignalP** >= 3.0 is an optional dependency to find signal peptides. For licensing reasons, no automatic dependency is managed.
- **tbl2asn** >= 21.0 is required. This dependency is not managed here. The reason is that versions are increasing very rapidly. The software can be downloaded from the NCBI (ftp) at the following address.
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/
- **BioPerl** >= 1.6 is required, but the dependency is not managed here, although it might in future. 
- **GNU Parallel** >= 20120322 is required but is shipped with Prokka and thus is not managed by the tool dependency system

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

- v0.2: added this readme file, supports prokka 1.7 and adds dependencies management.
- v0.1: initial release in the toolshed, supports prokka 1.6.


Copyright
---------

prokka is developed by  Torsten Seemann at Victorian Bioinformatics Consortium http://www.bioinformatics.net.au/. prokka is released under GPLv3 or later.

This wrapper is copyrighted by Lionel Guy, and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.