On Wed, Aug 7, 2013 at 3:41 AM, Rodolfo Aramayo <raram...@tamu.edu> wrote:
> On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>>
>> Looks like your BOOST is too new for BLAST 2.2.26+ (which
>> just recently became a problem on the Galaxy Tool Shed testing
>> system as well).
>>
>> In the short term I'm hoping to update the Tool Shed repository
>> to use the NCBI provided pre-compiled binaries. I'm in discussion
>> with Galaxy's Dave Bouvier about how best to do that, perhaps
>> with some relatively new functionality added to Galaxy. Next,
>> updating the BLAST+ version (and the unit tests to match).
>>
>> I would suggest right now you manually install BLAST+ using
>> the NCBI provided binaries.
>>
>> Peter
>
> Boost is a funny thing
> Changes a lot
> A package compiled with one Boost version might fail to compile with a
> newer one. I have seen it a lot
> You either have to download Boost and link to the specific version you
> want before compiling your package or provide pre-compiled binaries
> The question I have is: How many Galaxy packages have Boos as a
> dependency for compilation? and if the answer is: a lot, then would it
> be smart for Galaxy to have a place where it can keep versions of
> these commonly-used libraries so that they can be linked by packages
> that need to be compiled 'in-situ' or would it be just more efficient
> to provide pre-compiled binaries?
> Something tells me that pre-compiled binaries might not take full
> advantage of the hardware they are and that compiling is better...
> So, should ToolShed installation require automatic download of a set
> of pre-defined commonly-used libraries?

That's probably possible via a Tool Shed dependency,
Bjoern has been working on this on the Test Tool Shed:
http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_boost_1_53

Now under a shared IUC account:
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53

Peter
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