diff readme.rst @ 4:5c0030f52b83 draft

Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 . Update citation.

--- a/readme.rst	Mon Dec 09 04:58:14 2013 -0500
+++ b/readme.rst	Wed Jan 08 04:29:37 2014 -0500
@@ -11,30 +11,31 @@
 
 - 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 ).
+prokka tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see http://wiki.galaxyproject.org/Admin/Config/Jobs and http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
 
-If instead you are using an older Galaxy release, you should add a line
+If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool.
+
+If instead you are using an older Galaxy release, you should also add a line
 
   GALAXY_SLOTS=N; export GALAXY_SLOTS
 
-(where N is the number of threads allocated by the job runner) to the file
+(where N is the number of CPU cores allocated by the job runner for this tool) to the file
 
   <tool_dependencies_dir>/prokka/1.7/crs4/prokka/<hash_string>/env.sh
 
 Version history
 ---------------
 
+- Release 4 (prokka 1.3.0): Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 (requires Galaxy release_2013.11.04 or later). Update citation.
 - 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.