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/5064f618ec1c/README

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/5064f618ec1c/README

-rico

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