Mercurial > repos > bgruening > glimmer3
comparison readme.rst @ 0:841357e0acbf draft
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| author | bgruening |
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| date | Sat, 06 Jul 2013 10:09:30 -0400 |
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| children | b1ad88bbc5fa |
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| 1 ======================================= | |
| 2 Galaxy wrapper for Glimmer gene calling | |
| 3 ======================================= | |
| 4 | |
| 5 This wrapper is copyright 2012-2013 by Björn Grüning. | |
| 6 | |
| 7 This is a wrapper for the command line tool of Glimmer3_. | |
| 8 | |
| 9 .. _Glimmer: http://www.cbcb.umd.edu/software/glimmer/ | |
| 10 | |
| 11 Glimmer is a system for finding genes in microbial DNA, | |
| 12 especially the genomes of bacteria, archaea, and viruses. | |
| 13 Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated | |
| 14 Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. | |
| 15 | |
| 16 S. Salzberg, A. Delcher, S. Kasif, and O. White. Microbial gene identification using interpolated Markov models, Nucleic Acids Research 26:2 (1998), 544-548. | |
| 17 | |
| 18 A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Improved microbial gene identification with GLIMMER, Nucleic Acids Research 27:23 (1999), 4636-4641. | |
| 19 | |
| 20 A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007). | |
| 21 | |
| 22 | |
| 23 ============ | |
| 24 Installation | |
| 25 ============ | |
| 26 | |
| 27 Since version 0.2 the recommended installation procedure is via the `Galaxy Tool Shed`. | |
| 28 | |
| 29 .. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/glimmer3 | |
| 30 | |
| 31 To install Glimmer3 manually, please download Glimmer3 from:: | |
| 32 | |
| 33 http://www.cbcb.umd.edu/software/glimmer/glimmer302.tar.gz | |
| 34 | |
| 35 and follow the installation instructions. You can also use packages from your distribution like http://packages.debian.org/stable/science/tigr-glimmer | |
| 36 | |
| 37 To install the wrapper copy the glimmer3 folder in the galaxy tools | |
| 38 folder and modify the tools_conf.xml file to make the tool available to Galaxy. | |
| 39 For example:: | |
| 40 | |
| 41 <tool file="gene_prediction/tools/glimmer3/glimmer_w_icm.xml" /> | |
| 42 <tool file="gene_prediction/tools/glimmer3/glimmer_wo_icm.xml" /> | |
| 43 <tool file="gene_prediction/tools/glimmer3/glimmer_build-icm.xml" /> | |
| 44 | |
| 45 ======= | |
| 46 History | |
| 47 ======= | |
| 48 | |
| 49 - v0.1: Initial public release | |
| 50 - v0.2: Add tool shed integration | |
| 51 | |
| 52 =============================== | |
| 53 Wrapper Licence (MIT/BSD style) | |
| 54 =============================== | |
| 55 | |
| 56 Permission to use, copy, modify, and distribute this software and its | |
| 57 documentation with or without modifications and for any purpose and | |
| 58 without fee is hereby granted, provided that any copyright notices | |
| 59 appear in all copies and that both those copyright notices and this | |
| 60 permission notice appear in supporting documentation, and that the | |
| 61 names of the contributors or copyright holders not be used in | |
| 62 advertising or publicity pertaining to distribution of the software | |
| 63 without specific prior permission. | |
| 64 | |
| 65 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 66 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 67 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 68 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 69 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 70 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 71 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 72 OR PERFORMANCE OF THIS SOFTWARE. | |
| 73 |