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comparison README.rst @ 9:3b5eecc9551e draft

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author peterjc
date Fri, 25 Oct 2013 10:22:35 -0400
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8 the candidate effector protocol described in Jones et al. (2009). 8 the candidate effector protocol described in Jones et al. (2009).
9 9
10 See http://www.galaxyproject.org for information about the Galaxy Project. 10 See http://www.galaxyproject.org for information about the Galaxy Project.
11 11
12 12
13 Availability
14 ============
15
16 This workflow is available to download and/or install from the main
17 Galaxy Tool Shed:
18
19 http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
20
21 Test releases (which should not normally be used) are on the Test Tool Shed:
22
23 http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
24
25 Development is being done on github here:
26
27 https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow
28
29
13 Sample Data 30 Sample Data
14 =========== 31 ===========
15 32
16 This workflow was developed and run on several nematode species. For example, 33 This workflow was developed and run on several nematode species. For example,
17 try the protein set for Bursaphelenchus xylophilus (Kikuchi et al. 2011): 34 try the protein set for *Bursaphelenchus xylophilus* (Kikuchi et al. 2011):
18 35
19 ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.gz 36 ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.gz
20 37
21 You can upload this directly into Galaxy via this URL. Galaxy will handle 38 You can upload this directly into Galaxy via this URL. Galaxy will handle
22 removing the gzip compression to give you the FASTA protein file which has 39 removing the gzip compression to give you the FASTA protein file which has
28 ======== 45 ========
29 46
30 If you use this workflow directly, or a derivative of it, in work leading 47 If you use this workflow directly, or a derivative of it, in work leading
31 to a scientific publication, please cite: 48 to a scientific publication, please cite:
32 49
33 Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying 50 Cock, P.J.A. and Pritchard, L. (2014). Galaxy as a platform for identifying
34 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions: 51 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
35 Methods and Protocols (Second Edition)"; Methods in Molecular Biology. 52 Methods and Protocols (Second Edition)"; P. Birch, J. Jones, and J.I. Bos, eds.
36 Humana Press, Springer. In press. 53 Methods in Molecular Biology. Humana Press, Springer. ISBN 978-1-62703-985-7.
54 http://www.springer.com/life+sciences/plant+sciences/book/978-1-62703-985-7
37 55
38 Also consider citing: 56 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
57 Galaxy tools and workflows for sequence analysis with applications
58 in molecular plant pathology. PeerJ 1:e167
59 http://dx.doi.org/10.7717/peerj.167
39 60
40 Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004) 61 Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004)
41 Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95. 62 Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95.
42 http://dx.doi.org/10.1016/j.jmb.2004.05.028 63 http://dx.doi.org/10.1016/j.jmb.2004.05.028
43 64
50 Additional References 71 Additional References
51 ===================== 72 =====================
52 73
53 Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa. K., et al. (2011) 74 Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa. K., et al. (2011)
54 Genomic insights into the origin of parasitism in the emerging plant 75 Genomic insights into the origin of parasitism in the emerging plant
55 pathogen Bursaphelenchus xylophilus. PLoS Pathog 7: e1002219. 76 pathogen *Bursaphelenchus xylophilus*. PLoS Pathog 7: e1002219.
56 http://dx.doi.org/10.1371/journal.ppat.1002219 77 http://dx.doi.org/10.1371/journal.ppat.1002219
57 78
58 Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009) 79 Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009)
59 Identification and functional characterization of effectors in expressed 80 Identification and functional characterization of effectors in expressed
60 sequence tags from various life cycle stages of the potato cyst nematode 81 sequence tags from various life cycle stages of the potato cyst nematode
61 Globodera pallida. Mol Plant Pathol 10: 815–28. 82 *Globodera pallida*. Mol Plant Pathol 10: 815–28.
62 http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x 83 http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x
63
64
65 Availability
66 ============
67
68 This workflow is available to download and/or install from the main
69 Galaxy Tool Shed:
70
71 http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
72
73 Test releases (which should not normally be used) are on the Test Tool Shed:
74
75 http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
76
77 Development is being done on github here:
78
79 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow
80 84
81 85
82 Dependencies 86 Dependencies
83 ============ 87 ============
84 88
110 Developers 114 Developers
111 ========== 115 ==========
112 116
113 This workflow is under source code control here: 117 This workflow is under source code control here:
114 118
115 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow 119 https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow
116 120
117 To prepare the tar-ball for uploading to the Tool Shed, I use this: 121 To prepare the tar-ball for uploading to the Tool Shed, I use this:
118 122
119 $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga 123 $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga
120 124