Mercurial > repos > peterjc > rxlr_venn_workflow

annotate README.rst @ 8:2dfe8b788fb6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.1h, attempt to show image in README file
author peterjc
date Mon, 19 Aug 2013 13:22:30 -0400
parents 51aeb3d4799d
children d893133128d8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
1 This is package is a Galaxy workflow for comparing three RXLR prediction
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
2 methods with a Venn Diagram, and creates a FASTA file of any proteins
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
3 passing all three methods.
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
4
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
5 See http://www.galaxyproject.org for information about the Galaxy Project.
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
6
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
7
7
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
8 Sample Data
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
9 ===========
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
10
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
11 This workflow was developed and run on several Phytophthora species.
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
12 For example, try the "Phyca11" protein set for Phytophthora capsici:
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
13
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
14 http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
15
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
16 You can upload this directly into Galaxy via this URL. Galaxy will handle
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
17 removing the gzip compression to give you the FASTA protein file which
8
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
18 has 19,805 protein sequences. The expected results:
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
19
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
20 * 89 RXLRs using Whisson et al. (2007)
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
21 * 124 RXLRs using Win et al. (2007)
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
22 * 162 RXLRs using Bhattacharjee et al. (006)
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
23
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
24 Of these, only 79 sequences pass all three of the RXLR prediction tools,
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
25 while 19643 have no RXLR matches at all.
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
26
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
27 .. image:: Phyca11_example_output.png
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
28 :height: 400px
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
29 :width: 400px
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
30 :alt: RXLR Venn diagram using Phytophthora capsici (Phyca11)
7
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
31
51aeb3d4799d Uploaded v0.0.1g, add Phyca11 example to README
peterjc
parents: 6
diff changeset
32
6
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
33 Citation
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
34 ========
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
35
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
36 If you use this workflow directly, or a derivative of it, in work leading
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
37 to a scientific publication, please cite:
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
38
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
39 Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
40 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
41 Methods and Protocols (Second Edition)"; Methods in Molecular Biology.
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
42 Humana Press, Springer. In press.
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
43
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
44 Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007)
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
45 A translocation signal for delivery of oomycete effector proteins into
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
46 host plant cells. Nature 450:115-118.
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
47 http://dx.doi.org/10.1038/nature06203
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
48
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
49 Win, J., Morgan, W., Bos, J., et al. (2007)
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
50 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
51 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369.
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
52 http://dx.doi.org/10.1105/tpc.107.051037
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
53
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
54 Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006)
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
55 The malarial host-targeting signal is conserved in the Irish potato famine
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
56 pathogen. PLoS Pathogens 2(5):e50.
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
57 http://dx.doi.org/10.1371/journal.ppat.0020050
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
58
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
59
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
60 Availability
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
61 ============
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
62
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
63 This workflow is available to download and/or install from the main
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
64 Galaxy Tool Shed:
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
65
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
66 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
67
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
68 Test releases (which should not normally be used) are on the Test Tool Shed:
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
69
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
70 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
71
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
72 Development is being done on github here:
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
73
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
74 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
75
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
76
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
77 Dependencies
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
78 ============
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
79
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
80 These dependencies should be resolved automatically via the Galaxy Tool Shed:
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
81
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
82 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
83 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
84 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
85
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
86 However, at the time of writing those Galaxy tools have their own dependencies
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
87 required for this workflow which require manual installation (SignalP v3.0,
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
88 HMMER v2.0, and the R/Bioconductor package limma).
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
89
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
90
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
91 Developers
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
92 ==========
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
93
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
94 This workflow is under source code control here:
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
95
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
96 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
97
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
98 To prepare the tar-ball for uploading to the Tool Shed, I use this:
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
99
8
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
100 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga Phyca11_example_output.png
6
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
101
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
102 Check this,
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
103
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
104 $ tar -tzf rxlr_venn_workflow.tar.gz
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
105 README.rst
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
106 repository_dependencies.xml
b1047023ffbb Uploaded v0.0.1f, README file with clearer citation instructions.
peterjc
parents:
diff changeset
107 rxlr_venn_workflow.ga
8
2dfe8b788fb6 Uploaded v0.0.1h, attempt to show image in README file
peterjc
parents: 7
diff changeset
108 Phyca11_example_output.png