On Fri, Feb 20, 2015 at 3:56 PM, Lapointe, David <David.Lapointe@tufts.edu> wrote:

I tried installing biopython and dependancies from the toolshed but this does not seem to be functional even though these tools say INSTALLED.

How are you testing it? Any Galaxy copy of Biopython will not be available to the system Python.

Is there something that I should do that I missed? I sis better to installed them in the regular python fashion?

Any Galaxy tool which wants access to a Galaxy copy of Biopython needs to declare this as an explicit dependency. e.g. http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss Peter