On Tue, Jan 6, 2015 at 12:23 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Yes ;)
>
> Are you writing your own tool, or trying to install someone else's?
>
> There are two basic options,
>
> (1) Install Biopython into the default Python used when jobs are
> run. Simple, but manual - and you can only have one version.
> This is actually what we are still doing on our local Galaxy
> since we started before the second option as available.
>
> (2) Install Biopython via the ToolShed, using the dependency
> mechanism. This allows multiple versions of Biopython (or any
> Python library) to be installed in parallel, and Galaxy does the
> setup to ensure the declared dependency is on the Python
> path when your script is run. e.g.
>
> https://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
>
> declares a dependency on:
>
> https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_62
>
> (which in turn depends on NumPy etc).
>
> This reminds me, we are overdue to create a Galaxy ToolShed
> package for Biopython 1.65, I must do that...

Done,
https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_65

And for tool developers on the TestToolShed too,
https://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_65

Peter
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