Greg,

That's part of the issue.  Please try the following:

1) Direct your browser to http://toolshed.g2.bx.psu.edu/view/miller- lab/genome_diversity
2) Choose "33:5064f618ec1c" under Repository revision
3) View "README" under Repository README files - may contain important installation or license information

        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/

4) Choose "30:4188853b940b" under Repository revision
5) View "README" under Repository README files - may contain important installation or license information

        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 README in step #5 above is not the README for changeset revision 4188853b940b. It is showing the README for changeset revision 5064f618ec1c instead. This is because revision 5064f618ec1c is currently found on disk in .../galaxy_toolshed/database/ community_files/000/repo_200.

I would expect that when viewing a specific changeset revision of a repository in the tool shed, I would see the README files for that changeset revision. The relevant code can be found in build_readme_files_dict() in lib/tool_shed/util/readme_util.py. It reads the files in the mercurial working directory without ensuring that the working directory is at the requested changeset revision.

-rico

On Sep 22, 2013, at 7:26 AM, Greg Von Kuster wrote:

Hi Rico,

It looks like the files on disk simply did not have the hg update applied when the last changeset was committed.

g2cmnty@montana:~/galaxy_toolshed/database/community_files/000/ repo_200$ hg update
46 files updated, 0 files merged, 26 files removed, 0 files unresolved
g2cmnty@montana:~/galaxy_toolshed/database/community_files/000/ repo_200$ 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/ g2cmnty@montana:~/galaxy_toolshed/database/community_files/000/ repo_200$

Since the issue was not related to the Tool Shed's README utility, is was easy to "miss" it.

Is the content of the README file now what you expect?

Greg Von Kuster


On Sep 21, 2013, at 6:13 PM, Richard Burhans <r...@bx.psu.edu> wrote:

Greg,

On Sep 21, 2013, at 6:03 PM, Greg Von Kuster wrote:

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.

I believe that you are missing something. Please try the following experiment:

$ hg clone http://toolshed.g2.bx.psu.edu/repos/miller-lab/ genome_diversity
$ cd genome_diversity
$ hg update tip
$ 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/

$ hg update 4188853b940b
$ 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.

If we're still not on the same page after this, perhaps I can stop by your office sometime during the week.

-rico






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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