ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
739 stars 134 forks source link

Build system should use available deps instead of externals when they are available #1325

Open bzizou opened 3 months ago

bzizou commented 3 months ago

Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above.

Some package managers (Nix, Guix,...) are able to provide fixed dependencies, with pinned versions when needed and that should replace the use of some ext/ redistributed projects. If I'm not wrong, the cmake files of Spades are not picking the deps when they are available (for example zlib-ng, gtest,...) and are always using the ext directory. In some cases, this leads to build failures, for example when using the Musl libc. Thos build failure are avoided if the deps are provided by the package manager (because deps packages are already fixed for that libc). For more infrmations, you can check this PR discussion: https://github.com/NixOS/nixpkgs/pull/320502

Describe the solution you'd like

When for example zilb-ng is available and with a suitable version number, then use it in place of the one that has been redistributed into the ext directory

Describe alternatives you've considered

No response

Additional context

No response