Mercurial > repos > bjoern-gruening > trna_prediction
diff 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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children | 65d282ef088e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.txt Wed Jan 11 05:57:32 2012 -0500 @@ -0,0 +1,80 @@ +Galaxy wrapper for t-RNA prediction tools +========================================= + +This wrapper is copyright 2012 by Björn Grüning. + +This prepository contains wrapper for the command line tools of tRNAscan-SE and Arogorn. +http://lowelab.ucsc.edu/tRNAscan-SE/ +http://130.235.46.10/ARAGORN/ + + +Dean Laslett and Bjorn Canback +ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucl. Acids Res. (2004) 32(1): 11-16 +doi:10.1093/nar/gkh152 + +Todd M. Lowe and Sean R. Eddy +tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964 +doi:10.1093/nar/25.5.0955 + + + +Installation +============ + +Please download tRNAscan-SE from the following URL and follow the install instructions. + +http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz + +Arogorn can be download from: + +http://mbio-serv2.mbioekol.lu.se/ARAGORN/aragorn1.2.33.c +With a recent GNU-Compiler (gcc) you can compile it with the following command. + +gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.33.c + +Please include aragorn and tRNAscan-SE into your PATH. +export PATH=$PATH:/home/user/bin/aragorn/bin/ + + +To install the wrappers copy the files aragorn.xml and tRNAscan.xml in the galaxy tools +folder and modify the tools_conf.xml file to make the tool available to Galaxy. +For example add the following lines: + +<tool file="trna_prediction/aragorn.xml" /> +<tool file="trna_prediction/tRNAscan.xml" /> + + + +History +======= + +tRNAscan: +v0.1 - Initial public release + +aragorn: +v0.1 - Initial public release + + + + +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. +