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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).
author crs4
date Mon, 09 Dec 2013 04:58:14 -0500
parents 4bafaa074484
children b9fea998270a
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1 Copyright © 2013 CRS4 Srl. http://www.crs4.it/
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4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
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2 Copyright © 2013 Lionel Guy
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3 Created by:
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4 Paolo Uva <paolo.uva@crs4.it>
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5 Nicola Soranzo <nicola.soranzo@crs4.it>
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4bafaa074484 Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
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6 Lionel Guy <lionel.guy@icm.uu.se>
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7
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8 Permission is hereby granted, free of charge, to any person obtaining a
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9 copy of this software and associated documentation files (the
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10 "Software"), to deal in the Software without restriction, including
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11 without limitation the rights to use, copy, modify, merge, publish,
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12 distribute, sublicense, and/or sell copies of the Software, and to
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13 permit persons to whom the Software is furnished to do so, subject to
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14 the following conditions:
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16 The above copyright notice and this permission notice shall be included
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17 in all copies or substantial portions of the Software.
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19 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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20 OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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21 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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22 IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
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23 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
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24 TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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25 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.