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| author | rmarenco |
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| date | Thu, 18 Aug 2016 18:50:00 -0400 |
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| 1 Galaxy wrapper for GlimmerHMM | |
| 2 ===================================== | |
| 3 | |
| 4 This wrapper has been rewritten by Rémi Marenco in 2016 to fix issues, improve it and add the multi_fasta handling. It has been originally written by Björn Gruening. | |
| 5 | |
| 6 This is a wrapper for the command line tool of GlimmerHMM. | |
| 7 https://ccb.jhu.edu/software/glimmerhmm/ | |
| 8 | |
| 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, | |
| 10 additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes | |
| 11 Interpolated Markov Models for the coding and noncoding models. | |
| 12 Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single). | |
| 13 | |
| 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. | |
| 15 Pertea, M. and S. L. Salzberg (2002). "Computational gene finding in plants." Plant Molecular Biology 48(1-2): 39-48. | |
| 16 The Arabidopsis Genome Initiative, (2000) "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana", Nature. Dec 14; 408(6814):796-815. | |
| 17 Pertea, M., S. L. Salzberg, et al. (2000). "Finding genes in Plasmodium falciparum." Nature 404(6773): 34; discussion 34-5. | |
| 18 Salzberg, S. L., M. Pertea, et al. (1999). "Interpolated Markov models for eukaryotic gene finding." Genomics 59(1): 24-31. | |
| 19 | |
| 20 | |
| 21 Installation | |
| 22 ============ | |
| 23 | |
| 24 To install Glimmer3, please download GlimmerHMM from | |
| 25 | |
| 26 ftp://ccb.jhu.edu/pub/software/glimmerhmm | |
| 27 | |
| 28 and follow the installation instructions. | |
| 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. | |
| 30 | |
| 31 To install the wrapper copy the glimmerHMM folder in the galaxy tools | |
| 32 folder and modify the $GALAXY_ROOT/config/tool_conf.xml file to make the tool available to Galaxy. | |
| 33 For example: | |
| 34 | |
| 35 ```xml | |
| 36 <tool file="gene_prediction/tools/glimmerHMM/glimmerhmm_predict.xml" /> | |
| 37 <tool file="gene_prediction/tools/glimmerHMM/glimmerhmm_to_sequence.xml" /> | |
| 38 ``` | |
| 39 | |
| 40 You also need to use a trained organism by adding them as reference data in Galaxy: | |
| 41 | |
| 42 1. Add the *glimmer_hmm_trained_dir* data table to `tool_data_table_conf.xml` in `$GALAXY_ROOT/config/`: | |
| 43 | |
| 44 ```xml | |
| 45 <!-- glimmer_hmm trained_dir --> | |
| 46 <table name="glimmer_hmm_trained_dir" comment_char="#"> | |
| 47 <columns>value, name, path</columns> | |
| 48 <file path="tool-data/glimmer_hmm.loc" /> | |
| 49 </table> | |
| 50 ``` | |
| 51 | |
| 52 2. Add the `glimmer_hmm.loc` file referencing your trained organism, in `tool-data`. | |
| 53 You have a sample [`glimmer_hmm.loc.sample`] available in the repository to help you configuring it properly | |
| 54 3. Add your data in the chosen folder at step 2. You can get them from the GlimmerHMM tar, `$GLIMMERHMM/trained_dir` | |
| 55 | |
| 56 History | |
| 57 ======= | |
| 58 | |
| 59 - v3.0 - Add the Multi Fasta support | |
| 60 - v2.0 - Update by Rémi Marenco to make it work without having to modify the wrapper + add ability to select the species | |
| 61 - v0.1 - Initial public release | |
| 62 | |
| 63 | |
| 64 Wrapper Licence (MIT/BSD style) | |
| 65 =============================== | |
| 66 | |
| 67 Permission to use, copy, modify, and distribute this software and its | |
| 68 documentation with or without modifications and for any purpose and | |
| 69 without fee is hereby granted, provided that any copyright notices | |
| 70 appear in all copies and that both those copyright notices and this | |
| 71 permission notice appear in supporting documentation, and that the | |
| 72 names of the contributors or copyright holders not be used in | |
| 73 advertising or publicity pertaining to distribution of the software | |
| 74 without specific prior permission. | |
| 75 | |
| 76 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 77 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 78 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 79 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 80 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 81 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 82 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 83 OR PERFORMANCE OF THIS SOFTWARE. |