Hello Rico, I'm not seeing a problem here. The revision of the genome_diversity you're referring to is the repository tip on the main tool shed. The README file on disk has this content: g2cmnty@montana:~/galaxy_toolshed/database/community_files/000/repo_200$ cat README Source code for the executables needed by these tools can be found in the genome_diversity directory. Additionally, you'll need the following python modules: matplotlib (we used version 1.1.0) http://pypi.python.org/packages/source/m/matplotlib/ mechanize (we used version 0.2.5) http://pypi.python.org/packages/source/m/mechanize/ networkx (we used version 1.6) http://pypi.python.org/packages/source/n/networkx/ fisher (we used version 0.1.4) http://pypi.python.org/packages/source/f/fisher/ And the following software: ADMIXTURE (we used version 1.22) http://www.genetics.ucla.edu/software/admixture/ EIGENSOFT (we used version 3.0) http://genepath.med.harvard.edu/~reich/Software.htm PHAST (we used version 1.2.1) http://compgen.bscb.cornell.edu/phast/ QuickTree (we used version 1.1) http://www.sanger.ac.uk/resources/software/quicktree/ Images used in the tools' documentation are located in the static/images directory. Please copy these to the static/images directory in your Galaxy installation. and the browser displays the following for the same revision: README README Source code for the executables needed by these tools can be found in the genome_diversity directory. Additionally, you'll need the following python modules: matplotlib (we used version 1.1.0) http://pypi.python.org/packages/source/m/matplotlib/ mechanize (we used version 0.2.5) http://pypi.python.org/packages/source/m/mechanize/ networkx (we used version 1.6) http://pypi.python.org/packages/source/n/networkx/ fisher (we used version 0.1.4) http://pypi.python.org/packages/source/f/fisher/ And the following software: ADMIXTURE (we used version 1.22) http://www.genetics.ucla.edu/software/admixture/ EIGENSOFT (we used version 3.0) http://genepath.med.harvard.edu/reich/Software.htm PHAST (we used version 1.2.1) http://compgen.bscb.cornell.edu/phast/ QuickTree (we used version 1.1) http://www.sanger.ac.uk/resources/software/quicktree/ Images used in the tools' documentation are located in the static/images directory. Please copy these to the static/images directory in your Galaxy installation. In addition, the Readme container will display the correct content of a README file that is associated with the selected changeset revision. Can you provide specific changeset revisions of a repository where this is not the case? The following URL is not a proper URL for browsing a tool shed repository Readme file via a browser.
http://toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/file/5064f61...
Greg Von Kuster On Sep 20, 2013, at 4:26 PM, Richard Burhans <rico@bx.psu.edu> wrote:
It appears that the Tool Shed does not show the correct "readme" file content.
1) get_readme_files() in lib/galaxy/webapps/tool_shed/controllers/repository.py gets the correct metadata from the database 2) build_readme_files_dict() in lib/tool_shed/util/readme_util.py reads data from whatever revision happens to be there (not the requested revision)
As an example, compare the output from: http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=genome_diversity&owner=miller-lab&changeset_revision=5064f618ec1c and: http://toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/file/5064f61...
-rico
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