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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>.
author crs4
date Mon, 27 Oct 2014 06:45:52 -0400
parents b9fea998270a
children f5e44aad6498
comparison
equal deleted inserted replaced
5:b9fea998270a 6:3ad7ef0ba385
2 ============== 2 ==============
3 3
4 Warning 4 Warning
5 ------- 5 -------
6 6
7 Prokka includes custom databases and is thus about a 2.0 GB download! 7 Prokka includes custom databases and is thus about a 340 MB download!
8 8
9 Dependencies of Prokka which needs to be installed separately 9 Dependencies of Prokka which need 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 - 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.
18 .. _SignalP: http://www.cbs.dtu.dk/services/SignalP/ 18 .. _SignalP: http://www.cbs.dtu.dk/services/SignalP/
19 19
20 Configuration 20 Configuration
21 ------------- 21 -------------
22 22
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 ). 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 https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
24 24
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. 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 26
27 If instead you are using an older Galaxy release, you should also add a line 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 CPU cores allocated by the job runner for this tool) 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/1.10/crs4/prokka/<hash_string>/env.sh
34 34
35 Version history 35 Version history
36 --------------- 36 ---------------
37 37
38 - 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>.
38 - Release 5 (prokka 1.3.0): Fix Prokka 1.8 dependency installation. 39 - Release 5 (prokka 1.3.0): Fix Prokka 1.8 dependency installation.
39 - 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. 40 - 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.
40 - 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). 41 - 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).
41 - 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 . 42 - 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 .
42 - 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. 43 - 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.