diff README.rst @ 1:606da4e1d925 draft

README file with clearer citation instructions.

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+This is package is a Galaxy workflow for the identification of candidate
+secreted proteins from a given protein FASTA file.
+
+It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a
+strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001)
+on those, and selects only proteins without a predicted trans-membrane helix.
+This workflow was used in Kikuchi et al (2001), and is a simplification of
+the candidate effector protocol described in Jones et al (2009).
+
+See http://www.galaxyproject.org for information about the Galaxy Project.
+
+
+Citation
+========
+
+If you use this workflow directly, or a derivative of it, in work leading
+to a scientific publication, please cite:
+
+Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying
+candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
+Methods and Protocols (Second Edition)"; Methods in Molecular Biology.
+Humana Press, Springer. In press.
+
+Also consider citing:
+
+Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004)
+Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95.
+http://dx.doi.org/10.1016/j.jmb.2004.05.028
+
+Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. (2001)
+Predicting transmembrane protein topology with a hidden Markov model:
+application to complete genomes. J Mol Biol 305: 567- 580.
+http://dx.doi.org/10.1006/jmbi.2000.4315
+
+
+Additional References
+=====================
+
+Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa. K., et al. (2011)
+Genomic insights into the origin of parasitism in the emerging plant
+pathogen Bursaphelenchus xylophilus. PLoS Pathog 7: e1002219.
+http://dx.doi.org/10.1371/journal.ppat.1002219
+
+Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009)
+Identification and functional characterization of effectors in expressed
+sequence tags from various life cycle stages of the potato cyst nematode
+Globodera pallida. Mol Plant Pathol 10: 815–28.
+http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x
+
+
+Availability
+============
+
+This workflow is available to download and/or install from the main
+Galaxy Tool Shed:
+
+http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
+
+Test releases (which should not normally be used) are on the Test Tool Shed:
+
+http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
+
+Development is being done on github here:
+
+https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_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
+
+However, at the time of writing those Galaxy tools have their own
+dependencies required for this workflow which require manual
+installation (SignalP v3.0 and TMHMM v2.0).
+
+
+Developers
+==========
+
+This workflow is under source code control here:
+
+https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow
+
+To prepare the tar-ball for uploading to the Tool Shed, I use this:
+
+    $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga
+
+Check this,
+
+    $ tar -tzf secreted_protein_workflow.tar.gz 
+    README.rst
+    repository_dependencies.xml
+    secreted_protein_workflow.ga