Mercurial > repos > bgruening > trna_prediction
annotate readme.rst @ 2:358f58401cd6 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
| author | bgruening |
|---|---|
| date | Wed, 26 Jul 2017 10:14:05 -0400 |
| parents | d34f31cbc9dd |
| children |
| rev | line source |
|---|---|
| 0 | 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 | |
|
2
358f58401cd6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
bgruening
parents:
0
diff
changeset
|
70 - v0.4: added gff3 parser |
|
358f58401cd6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction commit cfb19d75629f02e0dea4475c16c016ed5510eb44
bgruening
parents:
0
diff
changeset
|
71 - v0.5: improved gff3 parser, now handles introns and full gene model |
| 0 | 72 |
| 73 | |
| 74 | |
| 75 Wrapper Licence (MIT/BSD style) | |
| 76 =============================== | |
| 77 | |
| 78 Permission to use, copy, modify, and distribute this software and its | |
| 79 documentation with or without modifications and for any purpose and | |
| 80 without fee is hereby granted, provided that any copyright notices | |
| 81 appear in all copies and that both those copyright notices and this | |
| 82 permission notice appear in supporting documentation, and that the | |
| 83 names of the contributors or copyright holders not be used in | |
| 84 advertising or publicity pertaining to distribution of the software | |
| 85 without specific prior permission. | |
| 86 | |
| 87 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 88 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 89 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 90 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 91 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 92 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 93 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 94 OR PERFORMANCE OF THIS SOFTWARE. | |
| 95 |