# HG changeset patch
# User iuc
# Date 1477746932 14400
# Node ID 6aa88a432ffc819490103f8ad12840e36cd78f07
# Parent  d004ca37843e0d10675b2e065cedb5e7c441d3e6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144

diff -r d004ca37843e -r 6aa88a432ffc readme.rst
--- a/readme.rst	Fri Oct 28 13:45:14 2016 -0400
+++ b/readme.rst	Sat Oct 29 09:15:32 2016 -0400
@@ -6,10 +6,20 @@
 
 Prokka includes custom databases and is thus about a 340 MB download!
 
+Dependencies of Prokka which need 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`_;
+- 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/
+.. _SignalP: http://www.cbs.dtu.dk/services/SignalP/
+
 Version history
 ---------------
 
-- Release 8 (prokka 1.11.1): Use Conda for installing tool dependencies, ToolShed dependencies are not supported anymore. Add a test. The tool is now maintained by the IUC.
 - Release 7 (prokka 1.11.0): Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3.
 - Release 6 (prokka 1.4.0): Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.
 - Release 5 (prokka 1.3.0): Fix Prokka 1.8 dependency installation.