Mercurial > repos > peterjc > secreted_protein_workflow

changeset 1:606da4e1d925 draft

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README file with clearer citation instructions.
author peterjc
date Mon, 19 Aug 2013 11:37:04 -0400
parents 0ec2a079f68d
children 3a0c0d1c388f
files README.rst README.txt repository_dependencies.xml
diffstat 3 files changed, 99 insertions(+), 27 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Aug 19 11:37:04 2013 -0400
@@ -0,0 +1,97 @@
+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
--- a/README.txt	Mon May 06 11:29:15 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-This Tool Shed Repository contains a workflow for the identification of candidate secreted proteins from a given protein FASATA file.
-
-It runs SignalP v3.0 and selects only proteins with a strong predicted signal peptide, and then runs TMHMM v2.0 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).
-
-Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, 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 JT, Kumar A, Pylypenko LA, Thirugnanasambandam A, Castelli L, 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
-
-Bendtsen JD, 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
-
-
-Availability
-============
-
-This workflow is available on the main Galaxy Tool Shed:
-http://toolshed.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
--- a/repository_dependencies.xml	Mon May 06 11:29:15 2013 -0400
+++ b/repository_dependencies.xml	Mon Aug 19 11:37:04 2013 -0400
@@ -1,7 +1,7 @@
 <?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" />
+    <repository changeset_revision="6abd809cefdd" name="tmhmm_and_signalp" owner="peterjc" toolshed="http://toolshed.g2.bx.psu.edu" />
     <!-- 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" />
+    <repository changeset_revision="abdd608c869b" name="seq_filter_by_id" owner="peterjc" toolshed="http://toolshed.g2.bx.psu.edu" />
 </repositories>