Mercurial > repos > peterjc > rxlr_venn_workflow
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Uploaded v0.0.1f, README file with clearer citation instructions.
author | peterjc |
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date | Mon, 19 Aug 2013 11:38:36 -0400 |
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children | 51aeb3d4799d |
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1 This is package is a Galaxy workflow for comparing three RXLR prediction |
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2 methods with a Venn Diagram, and creates a FASTA file of any proteins |
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3 passing all three methods. |
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4 |
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5 See http://www.galaxyproject.org for information about the Galaxy Project. |
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6 |
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7 |
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8 Citation |
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9 ======== |
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10 |
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11 If you use this workflow directly, or a derivative of it, in work leading |
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12 to a scientific publication, please cite: |
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13 |
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14 Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying |
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15 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions: |
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16 Methods and Protocols (Second Edition)"; Methods in Molecular Biology. |
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17 Humana Press, Springer. In press. |
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18 |
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19 Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007) |
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20 A translocation signal for delivery of oomycete effector proteins into |
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21 host plant cells. Nature 450:115-118. |
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22 http://dx.doi.org/10.1038/nature06203 |
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23 |
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24 Win, J., Morgan, W., Bos, J., et al. (2007) |
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25 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors |
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26 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369. |
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27 http://dx.doi.org/10.1105/tpc.107.051037 |
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28 |
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29 Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006) |
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30 The malarial host-targeting signal is conserved in the Irish potato famine |
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31 pathogen. PLoS Pathogens 2(5):e50. |
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32 http://dx.doi.org/10.1371/journal.ppat.0020050 |
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33 |
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34 |
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35 Availability |
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36 ============ |
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37 |
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38 This workflow is available to download and/or install from the main |
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39 Galaxy Tool Shed: |
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40 |
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41 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow |
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42 |
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43 Test releases (which should not normally be used) are on the Test Tool Shed: |
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44 |
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45 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow |
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46 |
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47 Development is being done on github here: |
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48 |
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49 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow |
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50 |
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51 |
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52 Dependencies |
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53 ============ |
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54 |
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55 These dependencies should be resolved automatically via the Galaxy Tool Shed: |
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56 |
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57 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp |
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58 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id |
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59 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list |
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60 |
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61 However, at the time of writing those Galaxy tools have their own dependencies |
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62 required for this workflow which require manual installation (SignalP v3.0, |
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63 HMMER v2.0, and the R/Bioconductor package limma). |
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64 |
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65 |
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66 Developers |
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67 ========== |
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68 |
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69 This workflow is under source code control here: |
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70 |
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71 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow |
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72 |
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73 To prepare the tar-ball for uploading to the Tool Shed, I use this: |
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74 |
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75 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga |
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76 |
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77 Check this, |
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78 |
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79 $ tar -tzf rxlr_venn_workflow.tar.gz |
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80 README.rst |
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81 repository_dependencies.xml |
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82 rxlr_venn_workflow.ga |