Hello Björn, If numpy is not required for compiling matplotlib components (i.e., matplotlib components just use numpy after installation), then you should be able to make this work using a complex repository dependency for numpy in your tool_dependencies.xml definition for matplotlib. The discussion for doing this is at http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_reposit... By the way, I noticed that revision 2:c5fbe4aa5a74 of your package_numpy_1_7 repository on the test tool shed includes the following contents. Is this the repository you are working with? Strangely, the repository dependency should be invalid because it should not be possible for a repository to define a dependency upon any revision of itself. You may have uncovered a way to do this using a tool dependency definition with a complex repository dependency. I'll look into this and make sure to provide a fix for the scenario you used. Instead of the above approach, your approach here should be to include only the tool_dependencies.cml definition file for installing only numpy version 1.7.1 in a repository named package_numpy_1_7_1 (use the full version in naming the repository). You should create a separate repository named package_matplotlib_1_2_1 that similarly contains a single tool_dependencies.xml file that (in addition to defining how to install and compile mtplotlib) defines a complex repository dependency on the package_numpy_1_7_1 repository as described in the wiki at the link above. This approach creates 2 separate orphan tool dependencies, the second of which (matplotlib) has a complex repository dependency on the first (numpy). When you install the package_matplotlib_1_2_1 repository and check the box for handling tool dependencies during the installation, it will install the package_numpy_1_7_1 repository and create a pointer to the numpy binary in the env.sh file within the package_matplotlib_1_2_1 repository environment. This enables matplotlib to locate the required version of numpy. I know this is a bit tricky, so please let me know if it still does not make sense. Thanks very much, Greg Von Kuster On Apr 15, 2013, at 3:29 PM, Björn Grüning wrote:
Hi,
is there a general rule to handle dependencies inside of tool_dependencies.xml?
Lets assume I write a matplotlib orphan tool_dependencies.xml file. matplotlib depends on numpy. Numpy has already a orphan definition.
Is there a way to include numpy as dependency inside the matplotlib-definition, so that I did not need to fetch and compile numpy inside of matplotlib?
I tried to specify it beforehand but that did not work.
Thanks! Bjoern
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