Mercurial > repos > peterjc > rxlr_venn_workflow

changeset 6:b1047023ffbb draft

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Uploaded v0.0.1f, README file with clearer citation instructions.
author peterjc
date Mon, 19 Aug 2013 11:38:36 -0400
parents 41d8f46e0343
children 51aeb3d4799d
files README.rst README.txt repository_dependencies.xml
diffstat 3 files changed, 83 insertions(+), 74 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Aug 19 11:38:36 2013 -0400
@@ -0,0 +1,82 @@
+This is package is a Galaxy workflow for comparing three RXLR prediction
+methods with a Venn Diagram, and creates a FASTA file of any proteins
+passing all three methods.
+
+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.
+
+Whisson, S.C., Boevink, C.V., Moleleki, L., et al. (2007)
+A translocation signal for delivery of oomycete effector proteins into
+host plant cells. Nature 450:115-118.
+http://dx.doi.org/10.1038/nature06203
+
+Win, J., Morgan, W., Bos, J., et al. (2007)
+Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
+of plant pathogenic oomycetes. The Plant Cell 19:2349-2369.
+http://dx.doi.org/10.1105/tpc.107.051037
+
+Bhattacharjee, S., Luisa Hiller, N., Liolios, K., et al. (2006)
+The malarial host-targeting signal is conserved in the Irish potato famine
+pathogen. PLoS Pathogens 2(5):e50.
+http://dx.doi.org/10.1371/journal.ppat.0020050
+
+
+Availability
+============
+
+This workflow is available to download and/or install from the main
+Galaxy Tool Shed:
+
+http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
+
+Test releases (which should not normally be used) are on the Test Tool Shed:
+
+http://testtoolshed.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).
+
+
+Developers
+==========
+
+This workflow is under source code control here:
+
+https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
+
+To prepare the tar-ball for uploading to the Tool Shed, I use this:
+
+    $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga
+
+Check this,
+
+    $ tar -tzf rxlr_venn_workflow.tar.gz
+    README.rst
+    repository_dependencies.xml
+    rxlr_venn_workflow.ga
--- a/README.txt	Mon Jul 08 13:00:36 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,73 +0,0 @@
-This is package is a Galaxy workflow for comparing three RXLR prediction
-methods with a Venn Diagram, and creates a FASTA file of any proteins
-passing all three methods.
-
-See http://www.galaxyproject.org for information about the Galaxy Project.
-
-
-References
-==========
-
-Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, et al. (2007)
-A translocation signal for delivery of oomycete effector proteins into
-host plant cells. Nature 450:115-118.
-http://dx.doi.org/10.1038/nature06203
-
-Joe Win, William Morgan, Jorunn Bos, et al. (2007)
-Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
-of plant pathogenic oomycetes. The Plant Cell 19:2349-2369.
-http://dx.doi.org/10.1105/tpc.107.051037
-
-Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, et al. (2006)
-The malarial host-targeting signal is conserved in the Irish potato famine
-pathogen. PLoS Pathogens 2(5):e50.
-http://dx.doi.org/10.1371/journal.ppat.0020050
-
-
-Availability
-============
-
-This workflow is available to download and/or install from the main
-Galaxy Tool Shed:
-
-http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
-
-Test releases (which should not normally be used) are on the Test Tool Shed:
-
-http://testtoolshed.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).
-
-
-Developers
-==========
-
-This workflow is under source code control here:
-
-https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
-
-To prepare the tar-ball for uploading to the Tool Shed, I use this:
-
-    $ tar -cf rxlr_venn_workflow.tar.gz README.txt repository_dependencies.xml rxlr_venn_workflow.ga
-
-Check this,
-
-    $ tar -tzf rxlr_venn_workflow.tar.gz
-    README.txt
-    repository_dependencies.xml
-    rxlr_venn_workflow.ga
--- a/repository_dependencies.xml	Mon Jul 08 13:00:36 2013 -0400
+++ b/repository_dependencies.xml	Mon Aug 19 11:38:36 2013 -0400
@@ -3,7 +3,7 @@
     <!-- Revision 15:6abd809cefdd on the main tool shed is v0.2.4, the current latest - but older should be OK -->
     <repository changeset_revision="4cd848c5590b" name="tmhmm_and_signalp" owner="peterjc" toolshed="http://testtoolshed.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 changeset_revision="66d1ca92fb38" name="seq_filter_by_id" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="00153c4efec3" name="seq_filter_by_id" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     <!-- Revisiion 2:c96bef0643dc on the main tool shed is v0.0.3, the current latest -->
     <repository changeset_revision="51fe47a5a803" name="venn_list" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>