Mercurial > repos > peterjc > rxlr_venn_workflow

comparison README.txt @ 5:41d8f46e0343 draft

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Uploaded v0.0.1e, README formatting changes
author peterjc
date Mon, 08 Jul 2013 13:00:36 -0400
parents 65d174589251
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4:25e0ffd4f762 5:41d8f46e0343
1 This Tool Shed Repository contains a workflow for comparing three RXLR 1 This is package is a Galaxy workflow for comparing three RXLR prediction
2 prediction methods with a Venn Diagram, and creates a FASTA file of any 2 methods with a Venn Diagram, and creates a FASTA file of any proteins
3 proteins passing all three methods. 3 passing all three methods.
4
5 See http://www.galaxyproject.org for information about the Galaxy Project.
4 6
5 7
6 References 8 References
7 ========== 9 ==========
8 10
9 Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, Anna O. Avrova, 11 Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, et al. (2007)
10 Juan G. Morales, Eleanor M. Gilroy, Miles R. Armstrong, Severine Grouffaud, 12 A translocation signal for delivery of oomycete effector proteins into
11 Pieter van West, Sean Chapman, Ingo Hein, Ian K. Toth, Leighton Pritchard 13 host plant cells. Nature 450:115-118.
12 and Paul R. J. Birch A translocation signal for delivery of oomycete
13 effector proteins into host plant cells. Nature 450:115-118, 2007.
14 http://dx.doi.org/10.1038/nature06203 14 http://dx.doi.org/10.1038/nature06203
15 15
16 Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, 16 Joe Win, William Morgan, Jorunn Bos, et al. (2007)
17 Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun.
18 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors 17 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
19 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369, 2007. 18 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369.
20 http://dx.doi.org/10.1105/tpc.107.051037 19 http://dx.doi.org/10.1105/tpc.107.051037
21 20
22 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, 21 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, et al. (2006)
23 Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar.
24 The malarial host-targeting signal is conserved in the Irish potato famine 22 The malarial host-targeting signal is conserved in the Irish potato famine
25 pathogen. PLoS Pathogens, 2(5):e50, 2006. 23 pathogen. PLoS Pathogens 2(5):e50.
26 http://dx.doi.org/10.1371/journal.ppat.0020050 24 http://dx.doi.org/10.1371/journal.ppat.0020050
27 25
28 26
29 Availability 27 Availability
30 ============ 28 ============
31 29
32 This workflow is available on the main Galaxy Tool Shed: 30 This workflow is available to download and/or install from the main
31 Galaxy Tool Shed:
32
33 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow 33 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
34 34
35 Test releases (which should not be used) are on the Test Tool Shed: 35 Test releases (which should not normally be used) are on the Test Tool Shed:
36
36 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow 37 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
37 38
38 Development is being done on github here: 39 Development is being done on github here:
40
39 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow 41 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
40 42
41 43
42 Dependencies 44 Dependencies
43 ============ 45 ============
59 61
60 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow 62 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
61 63
62 To prepare the tar-ball for uploading to the Tool Shed, I use this: 64 To prepare the tar-ball for uploading to the Tool Shed, I use this:
63 65
64 $ tar -cf rxlr_venn_workflow.tar.gz README.txt repository_dependencies.xml rxlr_venn_workflow.ga 66 $ tar -cf rxlr_venn_workflow.tar.gz README.txt repository_dependencies.xml rxlr_venn_workflow.ga
65 67
66 Check this, 68 Check this,
67 69
68 $ tar -tzf rxlr_venn_workflow.tar.gz 70 $ tar -tzf rxlr_venn_workflow.tar.gz
69 README.txt 71 README.txt
70 repository_dependencies.xml 72 repository_dependencies.xml
71 rxlr_venn_workflow.ga 73 rxlr_venn_workflow.ga