I want to publish our own tool to the Galaxy Tool Shed. Our tool is our own developed C++ program. Our compiled binaries may not necessarily run in Galaxy servers due to different OS platforms. How could I resolve the tool dependency of our own compiled binaries? Thank you.
Build up your packages using conda-forge. There is support for compilation using c, c++ and fortran compilers. See https://conda-forge.org/#contribute
There are many examples to get started, for example parmed is now on conda-forge and it started as a PR to staged recipes https://github.com/conda-forge/staged-recipes/pull/8736.