Hi Rico,

On Sep 21, 2013, at 5:56 PM, Richard Burhans <r...@bx.psu.edu> wrote:

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

Unless I am missing something, montana has revisions 5064f618ec1c on disk:

g2cmnty@montana:~/galaxy_toolshed/database/community_files/000/repo_200$ hg 
heads
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


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.



> 
> 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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