I am currently trying to use ProtK on our Galaxy installation. I have finally installed successfully ProtK on our sever by:
rvm install 1.9.3 --with-gcc=clang
rvm use 1.9.3
gem install protk
So, I can see all the *.rb file in the bin folder (/home/base/.rvm/gems/gems/protk-1.2.5/bin/).
We also have installed TPP on our sever (/g/software/src/TPP/bin/, for example).
But, when i try to run tandem_search.rb on galaxy, it shows ""Could not find X!Tandem executable" (ArgumentError)"
How do I let ProtK know where i installed TPP?

I have spent incredible time on this to try to make it work. Any idea or suggestions are very appreciated.

Thank you very much.

Best Regards,