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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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1 This is package is a Galaxy workflow for comparing three RXLR prediction
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2 methods with a Venn Diagram, and creates a FASTA file of any proteins
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3 passing all three methods.
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5 See http://www.galaxyproject.org for information about the Galaxy Project.
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8 References
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9 ==========
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11 Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, et al. (2007)
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12 A translocation signal for delivery of oomycete effector proteins into
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13 host plant cells. Nature 450:115-118.
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14 http://dx.doi.org/10.1038/nature06203
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16 Joe Win, William Morgan, Jorunn Bos, et al. (2007)
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17 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
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18 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369.
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19 http://dx.doi.org/10.1105/tpc.107.051037
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21 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, et al. (2006)
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22 The malarial host-targeting signal is conserved in the Irish potato famine
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23 pathogen. PLoS Pathogens 2(5):e50.
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24 http://dx.doi.org/10.1371/journal.ppat.0020050
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27 Availability
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28 ============
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30 This workflow is available to download and/or install from the main
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31 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 normally be used) are on the Test Tool Shed:
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37 http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
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38
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39 Development is being done on github here:
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41 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
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44 Dependencies
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45 ============
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47 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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48 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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49 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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50 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
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51
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52 However, at the time of writing those Galaxy tools have their own dependencies
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53 required for this workflow which require manual installation (SignalP v3.0,
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54 HMMER v2.0, and the R/Bioconductor package limma).
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57 Developers
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58 ==========
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59
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60 This workflow is under source code control here:
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61
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62 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
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64 To prepare the tar-ball for uploading to the Tool Shed, I use this:
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66 $ tar -cf rxlr_venn_workflow.tar.gz README.txt repository_dependencies.xml rxlr_venn_workflow.ga
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68 Check this,
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70 $ tar -tzf rxlr_venn_workflow.tar.gz
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71 README.txt
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72 repository_dependencies.xml
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73 rxlr_venn_workflow.ga