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comparison readme.rst @ 10:6aa88a432ffc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
author iuc
date Sat, 29 Oct 2016 09:15:32 -0400
parents d004ca37843e
children fd4b2f03cfc6
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9:d004ca37843e 10:6aa88a432ffc
4 Warning 4 Warning
5 ------- 5 -------
6 6
7 Prokka includes custom databases and is thus about a 340 MB download! 7 Prokka includes custom databases and is thus about a 340 MB download!
8 8
9 Dependencies of Prokka which need to be installed separately
10 -------------------------------------------------------------
11
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`_;
14 - SignalP_ >= 3.0 is an optional dependency to find signal peptides. For licensing reasons, it is not used in the tool wrapper.
15
16 .. _BioPerl: http://search.cpan.org/dist/BioPerl/
17 .. _XML::Simple: http://search.cpan.org/dist/XML-Simple/
18 .. _SignalP: http://www.cbs.dtu.dk/services/SignalP/
19
9 Version history 20 Version history
10 --------------- 21 ---------------
11 22
12 - Release 8 (prokka 1.11.1): Use Conda for installing tool dependencies, ToolShed dependencies are not supported anymore. Add a test. The tool is now maintained by the IUC.
13 - 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.
14 - 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>.
15 - Release 5 (prokka 1.3.0): Fix Prokka 1.8 dependency installation. 25 - Release 5 (prokka 1.3.0): Fix Prokka 1.8 dependency installation.
16 - 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. 26 - 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.
17 - 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). 27 - 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).