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author bgruening
date Thu, 05 Dec 2013 09:44:17 -0500
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26 ============ 26 ============
27 27
28 The recommended installation is by means of the toolshed_. 28 The recommended installation is by means of the toolshed_.
29 If you need to install it manually here is a short introduction. 29 If you need to install it manually here is a short introduction.
30 30
31 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/augustus 31 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/bgruening/augustus
32 32
33 33
34 Install or downlaod augustus from:: 34 Install or downlaod augustus from::
35 35
36 http://bioinf.uni-greifswald.de/augustus/binaries/ 36 http://bioinf.uni-greifswald.de/augustus/binaries/
57 ======= 57 =======
58 58
59 - v0.1: Initial public release 59 - v0.1: Initial public release
60 - v0.2: Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson) 60 - v0.2: Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson)
61 - v0.3: upgrade to augustus 2.7, added new organisms and new parameters, output additional sequence files 61 - v0.3: upgrade to augustus 2.7, added new organisms and new parameters, output additional sequence files
62 - v0.3.1: added parallelism and changed the output parameters from boolean to a select box
62 63
63 Wrapper Licence (MIT/BSD style) 64 Licence (MIT)
64 =============================== 65 =============
65 66
66 Permission to use, copy, modify, and distribute this software and its 67 Permission is hereby granted, free of charge, to any person obtaining a copy
67 documentation with or without modifications and for any purpose and 68 of this software and associated documentation files (the "Software"), to deal
68 without fee is hereby granted, provided that any copyright notices 69 in the Software without restriction, including without limitation the rights
69 appear in all copies and that both those copyright notices and this 70 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
70 permission notice appear in supporting documentation, and that the 71 copies of the Software, and to permit persons to whom the Software is
71 names of the contributors or copyright holders not be used in 72 furnished to do so, subject to the following conditions:
72 advertising or publicity pertaining to distribution of the software
73 without specific prior permission.
74 73
75 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL 74 The above copyright notice and this permission notice shall be included in
76 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED 75 all copies or substantial portions of the Software.
77 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
78 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
79 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
80 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
81 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
82 OR PERFORMANCE OF THIS SOFTWARE.
83 76
77 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
78 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
79 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
80 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
81 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
82 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
83 THE SOFTWARE.
84