Bioconda packaging compatibility changes requested

[james-edward-hart]

Hi remeta team!

I have been working on adding remeta v0.11.2 for easy install through bioconda, but there is a patch required to get it through. I'm going to submit the PR for the new bioconda recipe but here are the details of the patch necessary to build the software in this way:

The patch does the following things:

• preserves Conda-provided compiler flags instead of replacing CMAKE_CXX_FLAGS
• makes CMake search the Conda prefix for htslib, libdeflate, Boost, zlib, OpenSSL, bzip2, xz/lzma, curl, OpenBLAS, LAPACK, and LAPACKE
• links Boost dynamically and uses CMake’s Threads::Threads / ${CMAKE_DL_LIBS}
• adds a missing <utility> include
• updates a few Eigen references from Eigen::all to Eigen::placeholders::all for compatibility with the Eigen version available in Conda

The patch is packaging/build-system-only; it does not change REMETA’s algorithms or command-line behavior. The recipe smoke test builds REMETA, runs remeta --version, checks command and flag usage output, and runs remeta index-anno on a tiny bgzipped annotation file.

When or if you make these CMake changes are made I will update the recipe to remove the patch and build as corrected.

Thanks for building a very cool software!