I've done some investigating, and it looks like there is an irregularity with the installation of package_numpy_1_7, and somehow package_biopython_1_62 is not finding the (successfully) installed numpy dependency. I duplicated the dependency chain for seq_select_by_id on my local tool shed, and got the following error for biopython's tool dependency record when installing seq_select_by_id into my local Galaxy instance:

export PYTHONPATH=$PYTHONPATH:/var/galaxy/tool_dependencies/biopython/1.62/devteam/package_biopython_1_62/c3c8665cb0af/lib/python &&
                    export PATH=$PATH:$PATH_NUMPY &&
                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &&
python setup.py install --install-lib /var/galaxy/tool_dependencies/biopython/1.62/devteam/package_biopython_1_62/c3c8665cb0af/lib/python

STDOUT
running install

Numerical Python (NumPy) is not installed.

This package is required for many Biopython features.  Please install
it before you install Biopython. You can install Biopython anyway, but
anything dependent on NumPy will not work. If you do this, and later
install NumPy, you should then re-install Biopython.

You can find NumPy at http://numpy.scipy.org

Note that when I installed seq_select_by_id, numpy installed correctly, and PYTHONPATH was populated with the right values.

   --Dave B.

On 09/30/2013 09:10 AM, Bjoern Gruening wrote:
Am Montag, den 30.09.2013, 14:02 +0100 schrieb Peter Cock:
On Mon, Sep 30, 2013 at 1:58 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
Peter,

It looks like there may be a version conflict between package_numpy and
either a system numpy or the Galaxy numpy egg. I'll investigate and keep you
updated on my progress.

    --Dave B.

Thanks Dave,

If Tool authors can assume NumPy is already present via the Galaxy
numpy egg and/or the system Python's numpy, that might be simpler...

The question is how to import the eggs into the tools? Is that possible
at all? For example pysam is shipped with Galaxy right? But is there a
way to use it inside of a tool?
But I think even if that is possible we need separate pysam/numpy
repositories for reproducibility.

I agree with Björn, it's probably not a good idea to use Galaxy eggs in tools and their dependencies, since the egg versions can change at any time, which might impact reproducibilty.


Cheers,
Bjoern

Peter
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