On Tue, Apr 16, 2013 at 5:23 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi all,
>
> Galaxy has long had two very simple (but largely unused)
> dependency mechanisms in a tool's XML (pre-dating the
> tool shed), for binaries and Python modules, e.g.
>
> <requirements>
>      <requirement type="python-module">numpy</requirement>
>      <requirement type="binary">taxBuilder</requirement>
> </requirements>
>
> http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Crequirement.3E_tag_set
>
> This has since been supplemented by the Tool Shed centric
> package requirement mechanism.
>
> How can a tool declare a Python dependency, and have
> it installed automatically via the Tool Shed? Presumably
> it would have to end up as an egg in the Galaxy eggs
> folder, and not be installed under the default Python's
> PYTHONPATH?

Actually thinking about this on the way home, I had
that back to front - we do want to install the dependency
so that is it available to the system's default Python
(and that will not look at the Galaxy eggs folder).

The Galaxy Tool Shed dependency installer doesn't
have root does it? That would help for many install
issues for libraries etc at system level, not just for
Python but similarly for Perl, R, etc.

Peter
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