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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
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3:fffa1ae330ae 4:5c0030f52b83
9 Dependencies of Prokka which needs to be installed separately 9 Dependencies of Prokka which needs to be installed separately
10 ------------------------------------------------------------- 10 -------------------------------------------------------------
11 11
12 - Perl core modules: File\::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds; 12 - Perl core modules: File\::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
13 - Perl modules: Bio::SeqIO from BioPerl_ >= 1.6.900, `XML::Simple`_; 13 - Perl modules: Bio::SeqIO from BioPerl_ >= 1.6.900, `XML::Simple`_;
14 - tbl2asn_ >= 21.0 is required. This dependency is not managed here since versions are increasing very rapidly;
15 - SignalP_ >= 3.0 is an optional dependency to find signal peptides. For licensing reasons, it is not used in the tool wrapper. 14 - SignalP_ >= 3.0 is an optional dependency to find signal peptides. For licensing reasons, it is not used in the tool wrapper.
16 15
17 .. _BioPerl: http://search.cpan.org/dist/BioPerl/ 16 .. _BioPerl: http://search.cpan.org/dist/BioPerl/
18 .. _XML::Simple: http://search.cpan.org/dist/XML-Simple/ 17 .. _XML::Simple: http://search.cpan.org/dist/XML-Simple/
19 .. _tbl2asn: http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/
20 .. _SignalP: http://www.cbs.dtu.dk/services/SignalP/ 18 .. _SignalP: http://www.cbs.dtu.dk/services/SignalP/
21 19
22 Configuration 20 Configuration
23 ------------- 21 -------------
24 22
25 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 ). 23 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 ).
26 24
27 If instead you are using an older Galaxy release, you should add a line 25 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.
26
27 If instead you are using an older Galaxy release, you should also add a line
28 28
29 GALAXY_SLOTS=N; export GALAXY_SLOTS 29 GALAXY_SLOTS=N; export GALAXY_SLOTS
30 30
31 (where N is the number of threads allocated by the job runner) to the file 31 (where N is the number of CPU cores allocated by the job runner for this tool) to the file
32 32
33 <tool_dependencies_dir>/prokka/1.7/crs4/prokka/<hash_string>/env.sh 33 <tool_dependencies_dir>/prokka/1.7/crs4/prokka/<hash_string>/env.sh
34 34
35 Version history 35 Version history
36 --------------- 36 ---------------
37 37
38 - 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.
38 - 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). 39 - 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).
39 - 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 . 40 - 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 .
40 - 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. 41 - 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.
41 - Release 0 (prokka 1.0.0): Initial release in the Tool Shed. 42 - Release 0 (prokka 1.0.0): Initial release in the Tool Shed.
42 43