Hi Greg, > 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_repository_dependencies:_tool_dependency_definitions_that_contain_repository_dependency_definitions
Thanks! But it is required at compile time. > 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. Oh, ok. in revision 3 of both packages you should see, what I was trying. > 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 r > epository 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. Lets see if I got it right. repository_dependencies.xml will be pared first. The defined repo's and the included and populated system variables will be available in tool_dependencies.xml, which is parsed afterwards. Is that correct? I will try that. Thanks! Bjoern > 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 > > > > ___________________________________________________________ > > 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/ > ___________________________________________________________ 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/
