Hi Rico, On Sep 21, 2013, at 5:56 PM, Richard Burhans <rico@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 <burhans@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 <burhans@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/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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