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author rmarenco
date Thu, 14 Jul 2016 15:15:24 -0400
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1 Galaxy wrapper for GlimmerHMM
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2 =====================================
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4 This wrapper has been written in 2012 by Björn Grüning, and updated by Rémi Marenco in 2016.
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6 This is a wrapper for the command line tool of GlimmerHMM.
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7 https://ccb.jhu.edu/software/glimmerhmm/
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9 GlimmerHMM is a gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM,
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10 additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes
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11 Interpolated Markov Models for the coding and noncoding models.
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12 Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).
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14 Majoros, W.H., Pertea, M., and Salzberg, S.L. TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders Bioinformatics 20 2878-2879.
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15 Pertea, M. and S. L. Salzberg (2002). "Computational gene finding in plants." Plant Molecular Biology 48(1-2): 39-48.
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16 The Arabidopsis Genome Initiative, (2000) "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana", Nature. Dec 14; 408(6814):796-815.
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17 Pertea, M., S. L. Salzberg, et al. (2000). "Finding genes in Plasmodium falciparum." Nature 404(6773): 34; discussion 34-5.
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18 Salzberg, S. L., M. Pertea, et al. (1999). "Interpolated Markov models for eukaryotic gene finding." Genomics 59(1): 24-31.
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21 Installation
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22 ============
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24 To install Glimmer3, please download GlimmerHMM from
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26 ftp://ccb.jhu.edu/pub/software/glimmerhmm
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28 and follow the installation instructions.
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29 To extract the glimmerHMM predicted genes, the GFF Parser from Brad Chapman (ttp://github.com/chapmanb/bcbb/tree/master/gff) was used and is included.
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31 To install the wrapper copy the glimmerHMM folder in the galaxy tools
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32 folder and modify the $GALAXY_ROOT/config/tool_conf.xml file to make the tool available to Galaxy.
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33 For example:
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35 ```xml
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36 <tool file="gene_prediction/tools/glimmerHMM/glimmerhmm_predict.xml" />
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37 <tool file="gene_prediction/tools/glimmerHMM/glimmerhmm_to_sequence.xml" />
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38 ```
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40 You also need to use a trained organism by adding them as reference data in Galaxy:
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42 1. Add the *glimmer_hmm_trained_dir* data table to `tool_data_table_conf.xml` in `$GALAXY_ROOT/config/`:
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44 ```xml
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45 <!-- glimmer_hmm trained_dir -->
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46 <table name="glimmer_hmm_trained_dir" comment_char="#">
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47 <columns>value, name, path</columns>
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48 <file path="tool-data/glimmer_hmm.loc" />
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49 </table>
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50 ```
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52 2. Add the `glimmer_hmm.loc` file referencing your trained organism, in `tool-data`.
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53 You have a sample [`glimmer_hmm.loc.sample`] available in the repository to help you configuring it properly
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54 3. Add your data in the chosen folder at step 2. You can get them from the GlimmerHMM tar, `$GLIMMERHMM/trained_dir`
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56 History
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57 =======
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59 - v2.0 - Update by Rémi Marenco to make it work without having to modify the wrapper + add ability to select the species
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60 - v0.1 - Initial public release
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63 Wrapper Licence (MIT/BSD style)
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64 ===============================
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65
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66 Permission to use, copy, modify, and distribute this software and its
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67 documentation with or without modifications and for any purpose and
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68 without fee is hereby granted, provided that any copyright notices
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69 appear in all copies and that both those copyright notices and this
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70 permission notice appear in supporting documentation, and that the
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71 names of the contributors or copyright holders not be used in
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72 advertising or publicity pertaining to distribution of the software
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73 without specific prior permission.
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74
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75 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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76 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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77 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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78 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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79 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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80 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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81 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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82 OR PERFORMANCE OF THIS SOFTWARE.