Mercurial > repos > peterjc > rxlr_venn_workflow
comparison README.rst @ 3:1a1ab2f2b5b5 draft
README file with clearer citation instructions.
| author | peterjc |
|---|---|
| date | Mon, 19 Aug 2013 11:35:52 -0400 |
| parents | |
| children | 3c280e01b920 |
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| 2:fe5babf911e3 | 3:1a1ab2f2b5b5 |
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| 1 This is package is a Galaxy workflow for comparing three RXLR prediction | |
| 2 methods with a Venn Diagram, and creates a FASTA file of any proteins | |
| 3 passing all three methods. | |
| 4 | |
| 5 See http://www.galaxyproject.org for information about the Galaxy Project. | |
| 6 | |
| 7 | |
| 8 Citation | |
| 9 ======== | |
| 10 | |
| 11 If you use this workflow directly, or a derivative of it, in work leading | |
| 12 to a scientific publication, please cite: | |
| 13 | |
| 14 Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying | |
| 15 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions: | |
| 16 Methods and Protocols (Second Edition)"; Methods in Molecular Biology. | |
| 17 Humana Press, Springer. In press. | |
| 18 | |
| 19 Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007) | |
| 20 A translocation signal for delivery of oomycete effector proteins into | |
| 21 host plant cells. Nature 450:115-118. | |
| 22 http://dx.doi.org/10.1038/nature06203 | |
| 23 | |
| 24 Win, J., Morgan, W., Bos, J., et al. (2007) | |
| 25 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors | |
| 26 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369. | |
| 27 http://dx.doi.org/10.1105/tpc.107.051037 | |
| 28 | |
| 29 Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006) | |
| 30 The malarial host-targeting signal is conserved in the Irish potato famine | |
| 31 pathogen. PLoS Pathogens 2(5):e50. | |
| 32 http://dx.doi.org/10.1371/journal.ppat.0020050 | |
| 33 | |
| 34 | |
| 35 Availability | |
| 36 ============ | |
| 37 | |
| 38 This workflow is available to download and/or install from the main | |
| 39 Galaxy Tool Shed: | |
| 40 | |
| 41 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow | |
| 42 | |
| 43 Test releases (which should not normally be used) are on the Test Tool Shed: | |
| 44 | |
| 45 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow | |
| 46 | |
| 47 Development is being done on github here: | |
| 48 | |
| 49 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow | |
| 50 | |
| 51 | |
| 52 Dependencies | |
| 53 ============ | |
| 54 | |
| 55 These dependencies should be resolved automatically via the Galaxy Tool Shed: | |
| 56 | |
| 57 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp | |
| 58 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id | |
| 59 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list | |
| 60 | |
| 61 However, at the time of writing those Galaxy tools have their own dependencies | |
| 62 required for this workflow which require manual installation (SignalP v3.0, | |
| 63 HMMER v2.0, and the R/Bioconductor package limma). | |
| 64 | |
| 65 | |
| 66 Developers | |
| 67 ========== | |
| 68 | |
| 69 This workflow is under source code control here: | |
| 70 | |
| 71 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow | |
| 72 | |
| 73 To prepare the tar-ball for uploading to the Tool Shed, I use this: | |
| 74 | |
| 75 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga | |
| 76 | |
| 77 Check this, | |
| 78 | |
| 79 $ tar -tzf rxlr_venn_workflow.tar.gz | |
| 80 README.rst | |
| 81 repository_dependencies.xml | |
| 82 rxlr_venn_workflow.ga |