comparison readme.txt @ 0:b46d3df3eb9e

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author bjoern-gruening
date Wed, 11 Jan 2012 05:57:32 -0500
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1 Galaxy wrapper for t-RNA prediction tools
2 =========================================
3
4 This wrapper is copyright 2012 by Björn Grüning.
5
6 This prepository contains wrapper for the command line tools of tRNAscan-SE and Arogorn.
7 http://lowelab.ucsc.edu/tRNAscan-SE/
8 http://130.235.46.10/ARAGORN/
9
10
11 Dean Laslett and Bjorn Canback
12 ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16
13 doi:10.1093/nar/gkh152
14
15 Todd M. Lowe and Sean R. Eddy
16 tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964
17 doi:10.1093/nar/25.5.0955
18
19
20
21 Installation
22 ============
23
24 Please download tRNAscan-SE from the following URL and follow the install instructions.
25
26 http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz
27
28 Arogorn can be download from:
29
30 http://mbio-serv2.mbioekol.lu.se/ARAGORN/aragorn1.2.33.c
31 With a recent GNU-Compiler (gcc) you can compile it with the following command.
32
33 gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.33.c
34
35 Please include aragorn and tRNAscan-SE into your PATH.
36 export PATH=$PATH:/home/user/bin/aragorn/bin/
37
38
39 To install the wrappers copy the files aragorn.xml and tRNAscan.xml in the galaxy tools
40 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
41 For example add the following lines:
42
43 <tool file="trna_prediction/aragorn.xml" />
44 <tool file="trna_prediction/tRNAscan.xml" />
45
46
47
48 History
49 =======
50
51 tRNAscan:
52 v0.1 - Initial public release
53
54 aragorn:
55 v0.1 - Initial public release
56
57
58
59
60 Wrapper Licence (MIT/BSD style)
61 ===============================
62
63 Permission to use, copy, modify, and distribute this software and its
64 documentation with or without modifications and for any purpose and
65 without fee is hereby granted, provided that any copyright notices
66 appear in all copies and that both those copyright notices and this
67 permission notice appear in supporting documentation, and that the
68 names of the contributors or copyright holders not be used in
69 advertising or publicity pertaining to distribution of the software
70 without specific prior permission.
71
72 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
73 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
74 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
75 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
76 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
77 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
78 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
79 OR PERFORMANCE OF THIS SOFTWARE.
80