No it does not have root, and it is very important that we not install
anything at the system level since we need to maintain version
isolation. We should always be able to inject things into the
environment so that Python/Perl/R look in the right place.

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Tue, Apr 16, 2013 at 2:05 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 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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