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
comparison
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2:fe5babf911e3 3:1a1ab2f2b5b5
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