Greg,

To be more clear, montana has revision 4188853b940b on disk, which is not the 
tip revision, 5064f618ec1c.

g2cmnty@montana:~/galaxy_toolshed/database/community_files/000/repo_200$ hg 
summary
parent: 30:4188853b940b 
 Update to Miller Lab devshed revision eb4e61d024db
branch: default
commit: (clean)
update: 3 new changesets (update)

g2cmnty@montana:~/galaxy_toolshed/database/community_files/000/repo_200$ hg tip
changeset:   33:5064f618ec1c
tag:         tip
user:        Richard Burhans <burh...@bx.psu.edu>
date:        Fri Sep 20 14:01:30 2013 -0400
summary:     remove munkres dependency

Here's how you can see the correct version of the README file:

$ hg clone http://toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity
$ cd genome_diversity
$ hg update 5064f618ec1c
$ cat README
The Genome Diversity tools require the following software:
    ADMIXTURE  (we used version 1.22)  
http://www.genetics.ucla.edu/software/admixture/
    KING       (we used version 1.5)   http://people.virginia.edu/~wc9c/KING/

The galaxy code requests the readme info using the following:
        
http://toolshed.g2.bx.psu.edu/repository/get_readme_files?name=genome_diversity&owner=miller-lab&changeset_revision=5064f618ec1c

build_readme_files_dict() in lib/tool_shed/util/readme_util.py reads the README 
file in .../database/community_files/000/repo_200 which is revision 
4188853b940b, not 5064f618ec1c.

The code assumes that the version in .../database/community_files/000/repo_200 
is at the requested revision without checking.  This may be a correct 
assumption.  If so, there is a bug somewhere else causing the incorrect 
revision to be found in ../database/community_files/000/repo_200.

-rico

On Sep 20, 2013, at 10:38 PM, Greg Von Kuster wrote:

> 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/5064f618ec1c/README
> 
> Greg Von Kuster
> 
> 
> On Sep 20, 2013, at 4:26 PM, Richard Burhans <r...@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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> 


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