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annotate README.txt @ 3:65d174589251 draft

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Uploaded v0.0.1c, repository_dependencies.xml with implicit current toolshed & latest revision
author peterjc
date Mon, 08 Jul 2013 11:21:05 -0400
parents e99b1bbe44f8
children 41d8f46e0343
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1 This Tool Shed Repository contains a workflow for comparing three RXLR
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2 prediction methods with a Venn Diagram, and creates a FASTA file of any
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3 proteins passing all three methods.
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6 References
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7 ==========
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9 Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, Anna O. Avrova,
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10 Juan G. Morales, Eleanor M. Gilroy, Miles R. Armstrong, Severine Grouffaud,
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11 Pieter van West, Sean Chapman, Ingo Hein, Ian K. Toth, Leighton Pritchard
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12 and Paul R. J. Birch A translocation signal for delivery of oomycete
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13 effector proteins into host plant cells. Nature 450:115-118, 2007.
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14 http://dx.doi.org/10.1038/nature06203
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16 Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano,
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17 Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun.
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18 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
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19 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369, 2007.
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20 http://dx.doi.org/10.1105/tpc.107.051037
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22 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win,
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23 Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar.
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24 The malarial host-targeting signal is conserved in the Irish potato famine
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25 pathogen. PLoS Pathogens, 2(5):e50, 2006.
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26 http://dx.doi.org/10.1371/journal.ppat.0020050
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29 Availability
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30 ============
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31
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32 This workflow is available on the main Galaxy Tool Shed:
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33 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
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35 Test releases (which should not be used) are on the Test Tool Shed:
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36 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
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37
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38 Development is being done on github here:
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39 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
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42 Dependencies
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43 ============
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44
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45 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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46 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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47 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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48 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
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49
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50 However, at the time of writing those Galaxy tools have their own dependencies
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51 required for this workflow which require manual installation (SignalP v3.0,
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52 HMMER v2.0, and the R/Bioconductor package limma).
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55 Developers
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56 ==========
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57
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58 This workflow is under source code control here:
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59
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60 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
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62 To prepare the tar-ball for uploading to the Tool Shed, I use this:
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64 $ tar -cf rxlr_venn_workflow.tar.gz README.txt repository_dependencies.xml rxlr_venn_workflow.ga
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65
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66 Check this,
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68 $ tar -tzf rxlr_venn_workflow.tar.gz
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69 README.txt
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70 repository_dependencies.xml
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71 rxlr_venn_workflow.ga