Mercurial > repos > bgruening > trna_prediction
comparison readme.rst @ 0:d34f31cbc9dd draft
Uploaded
author | bgruening |
---|---|
date | Sat, 06 Jul 2013 10:37:13 -0400 |
parents | |
children | 358f58401cd6 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:d34f31cbc9dd |
---|---|
1 Galaxy wrapper for t-RNA prediction tools | |
2 ========================================= | |
3 | |
4 This wrapper is copyright 2012-2013 by Björn Grüning. | |
5 | |
6 This prepository contains wrapper for the command line tools of tRNAscan-SE_ and Arogorn_. | |
7 | |
8 .. _tRNAscan-SE: http://lowelab.ucsc.edu/tRNAscan-SE/ | |
9 .. _Arogorn: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ | |
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 The t-RNA prediction wrappers are available through the toolshed_ and can be automatically installed. | |
25 | |
26 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/trna_prediction | |
27 | |
28 For manuel installation, please download tRNAscan-SE from the following URL and follow the install instructions:: | |
29 | |
30 http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz | |
31 | |
32 Arogorn can be download from:: | |
33 | |
34 http://mbio-serv2.mbioekol.lu.se/ARAGORN/aragorn1.2.33.c | |
35 | |
36 With a recent GNU-Compiler (gcc) you can compile it with the following command:: | |
37 | |
38 gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.33.c | |
39 | |
40 Please include aragorn and tRNAscan-SE into your PATH:: | |
41 | |
42 export PATH=$PATH:/home/user/bin/aragorn/bin/ | |
43 | |
44 | |
45 To install the wrappers copy the files aragorn.xml and tRNAscan.xml in the galaxy tools | |
46 folder and modify the tools_conf.xml file to make the tool available to Galaxy. | |
47 For example add the following lines:: | |
48 | |
49 <tool file="trna_prediction/aragorn.xml" /> | |
50 <tool file="trna_prediction/tRNAscan.xml" /> | |
51 | |
52 | |
53 ======= | |
54 History | |
55 ======= | |
56 | |
57 tRNAscan: | |
58 | |
59 - v0.1: Initial public release | |
60 - v0.2: add fasta output | |
61 - v0.2.1: added tool-dependency | |
62 - v0.2.2: patch from Nicola Soranzo added | |
63 - v0.3: add unit tests, documentation improvements, bug fixes | |
64 | |
65 aragorn: | |
66 | |
67 - v0.1: Initial public release | |
68 - v0.2: added options, upgrade to 1.2.36, tool-dependency | |
69 - v0.3: add unit tests, documentation improvements | |
70 | |
71 | |
72 | |
73 Wrapper Licence (MIT/BSD style) | |
74 =============================== | |
75 | |
76 Permission to use, copy, modify, and distribute this software and its | |
77 documentation with or without modifications and for any purpose and | |
78 without fee is hereby granted, provided that any copyright notices | |
79 appear in all copies and that both those copyright notices and this | |
80 permission notice appear in supporting documentation, and that the | |
81 names of the contributors or copyright holders not be used in | |
82 advertising or publicity pertaining to distribution of the software | |
83 without specific prior permission. | |
84 | |
85 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
86 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
87 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
88 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
89 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
90 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
91 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
92 OR PERFORMANCE OF THIS SOFTWARE. | |
93 |