On Wed, Aug 7, 2013 at 3:41 AM, Rodolfo Aramayo <raramayo@tamu.edu> wrote:
On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock <p.j.a.cock@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