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1 Galaxy wrapper for RepeatMasker
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2 =====================================
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3
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4 This wrapper is copyright 2012 by Björn Grüning.
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5
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6 This is a wrapper for the command line tool of Glimmer3.
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7 http://www.cbcb.umd.edu/software/glimmer/
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8
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9 Glimmer is a system for finding genes in microbial DNA,
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10 especially the genomes of bacteria, archaea, and viruses.
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11 Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated
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12 Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
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13
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14 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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15 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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16 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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17
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18
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19
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20 Installation
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21 ============
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22
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23 To install Glimmer3, please download Glimmer3 from
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24
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25 http://www.cbcb.umd.edu/software/glimmer/glimmer302.tar.gz
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26
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27 and follow the installation instructions. You can also use packages from your distribution like
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28
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29 http://packages.debian.org/stable/science/tigr-glimmer
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30
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31
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32 To install the wrapper copy the glimmer3 folder in the galaxy tools
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33 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
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34 For example:
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35
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36 <tool file="gene_prediction/tools/glimmer3/glimmer3-main-wrapper.xml" />
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37 <tool file="gene_prediction/tools/glimmer3/glimmer_predict.xml" />
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38 <tool file="gene_prediction/tools/glimmer3/glimmer_orf_to_seq.xml" />
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39 <tool file="gene_prediction/tools/glimmer3/glimmer2gff.xml" />
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40 <tool file="gene_prediction/tools/glimmer3/gbktoorfWrapper.xml" />
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41 <tool file="gene_prediction/tools/glimmer3/glimmer_acgt_content.xml" />
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42 <tool file="gene_prediction/tools/glimmer3/glimmer3-build-icm-wrapper.xml" />
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43 <tool file="gene_prediction/tools/glimmer3/glimmer3-extract-wrapper.xml" />
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44 <tool file="gene_prediction/tools/glimmer3/glimmer3-long-orfs-wrapper.xml" />
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45
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46
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47 History
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48 =======
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49
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50 v0.1 - Initial public release
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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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