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annotate readme.rst @ 4:563743fcaae1 draft

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author lionelguy
date Thu, 05 Sep 2013 04:07:37 -0400
parents 2bb7c28ea68f
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2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
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1 Prokka wrapper
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2 ==============
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4 Warning
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5 -------
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7 Prokka comes with custom databases and is thus very large: **~2Gb**!
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9 Note
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10 ----
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12 - **infernal** >= 1.1rc4 is an optional dependency to find non-coding RNAs. An executable is shipped with prokka.
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
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13 - **SignalP** >= 3.0 is an optional dependency to find signal peptides. For licensing reasons, no automatic dependency is managed.
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14 - **tbl2asn** >= 21.0 is required. This dependency is not managed here. The reason is that versions are increasing very rapidly. The software can be downloaded from the `NCBI ftp site`_
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15 ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/
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16 - **BioPerl** >= 1.6 is required, but the dependency is not managed here, although it might in future.
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17 - **GNU Parallel** >= 20120322 is required but is shipped with Prokka and thus is not managed by the tool dependency system
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19 Version history
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20 ---------------
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22 - v0.2: added this readme file, supports prokka 1.7 and adds dependencies management.
2bb7c28ea68f Committed version 0.2: added dependency management and a readme file, and support prokka 1.7
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23 - v0.1: initial release in the toolshed, supports prokka 1.6.
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26 Copyright
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27 ---------
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29 prokka is developed by Torsten Seemann at Victorian Bioinformatics Consortium http://www.bioinformatics.net.au/. prokka is released under GPLv3 or later.
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31 This wrapper is copyrighted by Lionel Guy, and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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33 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
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35 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
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37 .. _`NCBI ftp site`://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/