On Tue, Sep 10, 2013 at 9:16 AM, Hans-philipp Brachvogel
<hans-philipp.brachvo...@student.uni-tuebingen.de> wrote:
> Hey Dave,
>
> thanks for the reply! Guess I wrote too much and explained badly what I
> meant. I had already tested the Managed Tool Dependencies, but my problem
> was that those only work for <requirement type="package">xyz</requirement>
>
> They do not handle <requirement type="binary"... or <requirement
> type="python-module", which is what I am looking for (beacuse of our special
> setting). Anyhow, I searched a bit and found in
> galaxy_dir/lib/galaxy/tools/__init__.py. at line 2671:
>
>
>     if requirement.type in [ 'package', 'set_environment' ]:
>         script_file, base_path, version =
> self.app.toolbox.dependency_manager.find_dep...
>
>
> So I changed that line to:
>
>     if requirement.type in [ 'package', 'set_environment', 'binary',
> 'python-module' ]
>
>
> This works, for me. If I have e.g.: <requirement
> type="python-module">rpy</requirement> I can now use
> dep_dir/rpy/default/env.sh to also load R into the environment.
>
> Now, I wonder if that change will have any bad consequences? I could not
> find anything about the requirement type 'binary' and 'python-module', what
> are they normally needed for? Could this be relevant when using tool-shed?
>
> Phil

These dependency declarations pre-date the Tool Shed and are
(as far as I know) ignored by the Tool Shed. They may currently
be non-functional, but I think they could be useful with a little
magic added to the Galaxy jobs to check the dependency as
part of the shell script submitted for the job (to give nice clear
failure errors about missing dependencies, rather than what
ever cryptic error the tool may give).

Peter
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