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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
author iuc
date Fri, 28 Oct 2016 13:03:19 -0400
parents f5e44aad6498
children d004ca37843e
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7:f5e44aad6498 8:392255fa7ab9
15 15
16 .. _BioPerl: http://search.cpan.org/dist/BioPerl/ 16 .. _BioPerl: http://search.cpan.org/dist/BioPerl/
17 .. _XML::Simple: http://search.cpan.org/dist/XML-Simple/ 17 .. _XML::Simple: http://search.cpan.org/dist/XML-Simple/
18 .. _SignalP: http://www.cbs.dtu.dk/services/SignalP/ 18 .. _SignalP: http://www.cbs.dtu.dk/services/SignalP/
19 19
20 Configuration
21 -------------
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 https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ).
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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 Version history 20 Version history
28 --------------- 21 ---------------
29 22
30 - 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. 23 - 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.
31 - 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>. 24 - 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>.
39 Version history of (now deprecated) Lionel Guy's wrapper: 32 Version history of (now deprecated) Lionel Guy's wrapper:
40 33
41 - prokka 1.1.0: Merge the wrappers by CRS4 and Lionel Guy. Add COPYING file with MIT license. Make all params optional. Add 'gffver' param. Correctly quote text params in command. Use float type for 'evalue' param. Describe output files in help. Upgrade BLAST+ dependency to v. 2.2.28. Depend on package_aragorn_1_2_36 instead of trna_prediction. Depend on package_prodigal_2_60 instead of prodigal. Depend on package_barrnap_0_2 instead of barrnap. Add PROKKA_SITE_OPTIONS to env.sh and remove 'cpus' param. 34 - prokka 1.1.0: Merge the wrappers by CRS4 and Lionel Guy. Add COPYING file with MIT license. Make all params optional. Add 'gffver' param. Correctly quote text params in command. Use float type for 'evalue' param. Describe output files in help. Upgrade BLAST+ dependency to v. 2.2.28. Depend on package_aragorn_1_2_36 instead of trna_prediction. Depend on package_prodigal_2_60 instead of prodigal. Depend on package_barrnap_0_2 instead of barrnap. Add PROKKA_SITE_OPTIONS to env.sh and remove 'cpus' param.
42 - prokka 0.2: Added this readme file. Support Prokka 1.7. Add dependencies management. 35 - prokka 0.2: Added this readme file. Support Prokka 1.7. Add dependencies management.
43 - prokka 0.1: Initial release in the Tool Shed, supports Prokka 1.6. 36 - prokka 0.1: Initial release in the Tool Shed, supports Prokka 1.6.
44
45 Development
46 -----------
47
48 Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!