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0
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1 =======================================
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2 Galaxy wrapper for Glimmer gene calling
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3 =======================================
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4
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5 This wrapper is copyright 2012-2013 by Björn Grüning.
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6
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7 This is a wrapper for the command line tool of Glimmer3_.
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8
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2
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9 .. _Glimmer3: http://www.cbcb.umd.edu/software/glimmer/
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0
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10
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11 Glimmer is a system for finding genes in microbial DNA,
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12 especially the genomes of bacteria, archaea, and viruses.
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13 Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated
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14 Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
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15
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2
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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.
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0
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17
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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.
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19
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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).
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0
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21
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22
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23 ============
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24 Installation
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25 ============
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26
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27 Since version 0.2 the recommended installation procedure is via the `Galaxy Tool Shed`.
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28
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29 .. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/glimmer3
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30
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31 To install Glimmer3 manually, please download Glimmer3 from::
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32
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33 http://www.cbcb.umd.edu/software/glimmer/glimmer302.tar.gz
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34
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35 and follow the installation instructions. You can also use packages from your distribution like http://packages.debian.org/stable/science/tigr-glimmer
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36
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37 To install the wrapper copy the glimmer3 folder in the galaxy tools
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38 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
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39 For example::
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40
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41 <tool file="gene_prediction/tools/glimmer3/glimmer_w_icm.xml" />
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42 <tool file="gene_prediction/tools/glimmer3/glimmer_wo_icm.xml" />
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43 <tool file="gene_prediction/tools/glimmer3/glimmer_build-icm.xml" />
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44
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45 =======
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46 History
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47 =======
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48
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49 - v0.1: Initial public release
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50 - v0.2: Add tool shed integration
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51
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52 ===============================
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53 Wrapper Licence (MIT/BSD style)
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54 ===============================
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55
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56 Permission to use, copy, modify, and distribute this software and its
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57 documentation with or without modifications and for any purpose and
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58 without fee is hereby granted, provided that any copyright notices
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59 appear in all copies and that both those copyright notices and this
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60 permission notice appear in supporting documentation, and that the
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61 names of the contributors or copyright holders not be used in
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62 advertising or publicity pertaining to distribution of the software
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63 without specific prior permission.
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64
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65 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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66 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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67 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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68 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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69 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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70 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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71 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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72 OR PERFORMANCE OF THIS SOFTWARE.
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73
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