diff README.rst @ 6:b1047023ffbb draft

Uploaded v0.0.1f, README file with clearer citation instructions.

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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