Mercurial > repos > peterjc > rxlr_venn_workflow
view README.rst @ 3:1a1ab2f2b5b5 draft
README file with clearer citation instructions.
author | peterjc |
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date | Mon, 19 Aug 2013 11:35:52 -0400 |
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children | 3c280e01b920 |
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This is package is a Galaxy workflow for comparing three RXLR prediction methods with a Venn Diagram, and creates a FASTA file of any proteins passing all three methods. See http://www.galaxyproject.org for information about the Galaxy Project. Citation ======== If you use this workflow directly, or a derivative of it, in work leading to a scientific publication, please cite: Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions: Methods and Protocols (Second Edition)"; Methods in Molecular Biology. Humana Press, Springer. In press. Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007) A translocation signal for delivery of oomycete effector proteins into host plant cells. Nature 450:115-118. http://dx.doi.org/10.1038/nature06203 Win, J., Morgan, W., Bos, J., et al. (2007) Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. The Plant Cell 19:2349-2369. http://dx.doi.org/10.1105/tpc.107.051037 Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006) The malarial host-targeting signal is conserved in the Irish potato famine pathogen. PLoS Pathogens 2(5):e50. http://dx.doi.org/10.1371/journal.ppat.0020050 Availability ============ This workflow is available to download and/or install from the main Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow Test releases (which should not normally be used) are on the Test Tool Shed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow Development is being done on github here: https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow Dependencies ============ These dependencies should be resolved automatically via the Galaxy Tool Shed: * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list However, at the time of writing those Galaxy tools have their own dependencies required for this workflow which require manual installation (SignalP v3.0, HMMER v2.0, and the R/Bioconductor package limma). Developers ========== This workflow is under source code control here: https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow To prepare the tar-ball for uploading to the Tool Shed, I use this: $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga Check this, $ tar -tzf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga