Hello Peter and Bjoern,

Can you clarify the "tool shed bug" to which you are referring with the 
statement:

> Still that TS bug needs to be fixed I think before the next stable
> release.

I'll take a look as soon as I get clarification.

Thanks!

On Aug 12, 2013, at 11:31 AM, Bjoern Gruening <bjoern.gruen...@gmail.com> wrote:

> On Mon, 2013-08-12 at 16:26 +0100, Peter Cock wrote:
>> On Mon, Aug 12, 2013 at 4:19 PM, Bjoern Gruening
>> <bjoern.gruen...@gmail.com> wrote:
>>> Hi Peter,
>>> 
>>>> 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)?
>>> 
>>> No that is correct, in that case we can omit the
>>> prior_installation_required=True flag for matplotlib.
>> 
>> OK, good. Thanks for clarifying that.
>> 
>>>> ------------------------------------------------------------------
>>>> 
>>>> 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.
>>> 
>>> I though a full fledged biopython would be better than a trimmed
>>> version. But your are the biopython expert. If you think the developer
>>> should take care of it, than I will eliminate the dependencies.
>>> My concern was, that if you use biopython and plot your genome you
>>> normally do not know that you need reportlab (because it come with
>>> biopython on most of the distributions). Actually in my github account I
>>> have the reportlab dependency included (but commented out).
>>> 
>>> I think its up to you. I do not mind.
>> 
>> It rather depends on how the Biopython you are using was
>> installed, and if the installation route took care of these
>> soft/recommended dependencies or not.
>> 
>> My inclination is to leave this to the Galaxy tool author to
>> make explicit when packaging their tool. If they forget, then
>> the script calling Biopython should fail with an indicative
>> ImportError or in some cases are more precise error
>> about what exactly is missing.
>> 
>> i.e. Lets have NumPy as the only dependency in the
>> Galaxy package for Biopython.
>> 
>> This has practical advantages like right now were a
>> problem with the 'soft' dependency on matplotlib is
>> blocking me from installing the Biopython package.
> 
> Ok, I removed the soft dependencies and uploaded it again.
> Still that TS bug needs to be fixed I think before the next stable
> release.
> 
>> Regards,
>> 
>> Peter
> 
> 
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