Mercurial > repos > peterjc > rxlr_venn_workflow
changeset 0:0e7c07ff11f9 draft
Uploaded v0.0.1, includes README file and dependencies.
| author | peterjc |
|---|---|
| date | Mon, 06 May 2013 14:02:20 -0400 |
| parents | |
| children | d4e4464a8f88 |
| files | README.txt repository_dependencies.xml rxlr_venn_workflow.ga |
| diffstat | 3 files changed, 517 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Mon May 06 14:02:20 2013 -0400 @@ -0,0 +1,37 @@ +This Tool Shed Repository contains a workflow for comparing three RXLR prediction methods with a Venn Diagram, and creates a FASTA file of any proteins passing all three methods. + + +References +========== + +Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, Anna O. Avrova, Juan G. Morales, Eleanor M. Gilroy, Miles R. Armstrong, Severine Grouffaud, Pieter van West, Sean Chapman, Ingo Hein, Ian K. Toth, Leighton Pritchard and Paul R. J. Birch A translocation signal for delivery of oomycete effector proteins into host plant cells. Nature 450:115-118, 2007. +http://dx.doi.org/10.1038/nature06203 + +Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun. Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. The Plant Cell 19:2349-2369, 2007. +http://dx.doi.org/10.1105/tpc.107.051037 + +Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar. The malarial host-targeting signal is conserved in the Irish potato famine pathogen. PLoS Pathogens, 2(5):e50, 2006. +http://dx.doi.org/10.1371/journal.ppat.0020050 + + +Availability +============ + +This workflow is available on the main Galaxy Tool Shed: +http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow + +Development is being done on github here: +https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow + + +Dependencies +============ + +These dependencies should be resolved automatically via the Galaxy Tool Shed: + * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp + * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id + * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list + +However, at the time of writing those Galaxy tools have their own dependencies +required for this workflow which require manual installation (SignalP v3.0, +HMMER v2.0, and the R/Bioconductor package limma).
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon May 06 14:02:20 2013 -0400 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<repositories description="This requires my SignalP and TMHMM wrapers, and my FASTA filtering tool."> + <!-- Revision 15:6abd809cefdd on the main tool shed is v0.2.4, the current latest - but older should be OK --> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="tmhmm_and_signalp" owner="peterjc" changeset_revision="6abd809cefdd" /> + <!-- Revision 2:abdd608c869b on the main tool shed is v0.0.5, the current latest - but older should be OK --> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="seq_filter_by_id" owner="peterjc" changeset_revision="abdd608c869b" /> + <!-- Revision 0:baf7031d470e on the main tool shed is v0.0.3, currently the only revision --> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="venn_list " owner="peterjc" changeset_revision="baf7031d470e" /> +</repositories>
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