Mercurial > repos > crs4 > prokka
diff readme.rst @ 4:5c0030f52b83 draft
Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 . Update citation.
author | crs4 |
---|---|
date | Wed, 08 Jan 2014 04:29:37 -0500 |
parents | fffa1ae330ae |
children | b9fea998270a |
line wrap: on
line diff
--- 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.