Mercurial > repos > bgruening > trna_prediction

comparison readme.rst @ 0:d34f31cbc9dd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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