Mercurial > repos > bjoern-gruening > trna_prediction
comparison readme.txt @ 0:b46d3df3eb9e
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author | bjoern-gruening |
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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 |