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 <[email protected]> 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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
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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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
