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)?
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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