Hi Bjoern (& Greg),

RE: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61

I'm wondering why in the Biopython package dependencies
matplotlib is currently marked as prior installation required? i.e.

    <package name="numpy" version="1.7.1">
        <repository changeset_revision="c75482be1d3a"
name="package_numpy_1_7" owner="iuc"
prior_installation_required="True"
toolshed="http://toolshed.g2.bx.psu.edu"; />
    </package>
    <package name="matplotlib" version="1.2.1">
        <repository changeset_revision="9d164359606b"
name="package_matplotlib_1_2" owner="iuc"
prior_installation_required="True"
toolshed="http://toolshed.g2.bx.psu.edu"; />
    </package>

Biopython needs NumPy pre-installed because Biopython has
some C code which must be compiled against the NumPy
headers.

However, all the other Biopython Python dependencies are
soft in the sense that the 3rd Python libraries just need to
be available at run time (e.g. via $PYTHONPATH).

Have I misunderstood the function of the Galaxy Tool Shed
term prior_installation_required, or can we omit this and
have it default to prior_installation_required="False" for
matplotlib (and other similar cases)?

------------------------------------------------------------------

More generally, if that is the case, I would probably opt
to make the Biopython package only depend on numpy,
and leave declaring soft dependencies (or recommended
packages in the terminology of some Linux distributions)
down to the package/tool calling Biopython.

For instance, my sequence manipulation tools which
use just core Biopython can depend on just the main
Biopython package.

Another tool which uses Biopython and matplotlib to
produce a graph would depend on both Biopython and
the matplotlib packages.

Another tool which uses Biopython's GenomeDiagram to
produce a figure would depend on both Biopython and
the (not yet written) ReportLab packages.

etc.

Peter
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