I've duplicated the installation error on the scipy tool dependency, and will be looking into the cause. Thanks for the report.

   --Dave B.

On 8/15/13 09:01:17.000, Bjoern Gruening wrote:
Hi Dave,

the bug is unfortunately still present in the latest Galaxy version.

If you try to install you will end
up with an error, because numpy is not found. That error appears because
scipy was uploaded and afterwards numpy was changed. The consequence is
that scipy references on old (not installable) version of numpy and

I would expect that scipy is always looking for the latest version of
numpy regardless of what is specified in the numpy XML file. Is that
assumption wrong? That would raise the question if revisions are still
needed for orphan-tool-dependencies or 'Tool dependency definition'.

Is that bug easy to fix? Or do I need to upload all my repositories in
the right order again? That would be the consequence, because otherwise
I do not get the revision tag updated.


Peter, Björn,

The August Galaxy release is out, and the template_command is now in the
stable repository and branch. Regarding matplotlib and numpy, I
currently only see matplotlib depending on the 74c21f9bdc39 revision of
numpy. Is this still an issue, or has it been resolved?

     --Dave B.

On 8/12/13 11:36:00.000, Bjoern Gruening wrote:
On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening
<> wrote:
On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote:
Maybe I should retitle this thread...

On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock <> wrote:

Thank you - installing the NumPy package now works for me,

I'm moving on to something odd with matplotlib instead...


There are currently two revisions to the main Tool Shed
package for numpy,

Rev 0: c75482be1d3a - needs not-yet-released features
Rev 1: 74c21f9bdc39 - simplified

I'm trying to install a package dependent on this via
matplotlib - but installing the matplotlib package fails:

This is something odd, why does it think it needs to install
the rev 0 c75482be1d3a version of package_numpy_1_7?
See screenshot, except here:

Repository dependencies - installation of these additional
repositories is required
Name  Revision        Owner   Installation status
package_freetype_2_4  8761091302c4    iuc     Installed
package_numpy_1_7     74c21f9bdc39    iuc     Installed
package_numpy_1_7     c75482be1d3a    iuc     Uninstalled

Yes, the matplotlib tool_dependencies.xml does list the
original revision:

      <package name="numpy" version="1.7.1">
         <repository changeset_revision="c75482be1d3a"
name="package_numpy_1_7" owner="iuc"
toolshed=""; />
      <package name="freetype" version="2.4.11">
          <repository changeset_revision="8761091302c4"
name="package_freetype_2_4" owner="iuc"
toolshed=""; />

But I thought as a "Tool dependency definition" only the
tip revision is ever used?

That is also what I understood, regardless of the revision there is only
one install able revision. But I guess the TS is generating the path to
numpy from the <package> tag and that points to an old non existing

Hmm. Something for Greg to look at then.

After attempting to install this, the status is "Installed, missing
repository dependencies" and this oddity about wanting two
revisions of NumPy persists.

The actual failure appears to be in compiling matplotlib itself...
I don't think it is finding the NumPy installation.

Is it possible to view the INSTALLATION.log from within the
Galaxy Admin web interface?

Yes you should see all installed files/folder and the INSTALLATION.log
in your web browser.

Can you give me a little more information on how to see
this from within Galaxy?

1. Open my Galaxy instance and log in,
2. Click on "Admin" from top menu
3. Click on "Manage installed tool shed repositories" on left
4. Select repository of interest

5. Click, "Manage tool dependencies"
6. Choose one of the dependencies

There should be a tree like structure to navigate to your
INSTALLATION.log file besides your file.

At this point the repository drop down menus I see are
"Get updates" and "Delete or inactivate". I must be looking
in the wrong place?

I can reproduce it here and it fails because of numpy.

OK, that's good - it sounds like the rival revision problem
is what is going wrong.

One fix to get it working is to upload again biopython.

Good plan - as discussed here:


Thank you,


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