Bascet (Bacterial Single CEll Toolkit)

Bascet is a complete solution for single-cell analysis, with focus on microbial analysis. It is however design to also do RNA-seq, ATAC-seq (you-name-it), agnostic from the instrument used. It has also been designed to analyze large numbers of bulk samples in a manner analogous to single-cell analysis (i.e. with a focus on clustering and data-driven analysis).

Bascet is an advanced command-line tool aimed primarily to be used through the Zorn R library, which offers multi-node compute capability and ease of use.

Most users will prefer to use Zorn. For more information, follow this link: https://henriksson-lab.github.io/zorn/

Cross-compiling

Use the helper scripts instead of the Makefile:

make install_cross
./scripts/build-linux.sh x86_64-unknown-linux-gnu
./scripts/build-windows.sh x86_64-pc-windows-gnu
./scripts/build-macos.sh x86_64-apple-darwin
./scripts/build-macos.sh aarch64-apple-darwin
./scripts/build-macos.sh universal

Notes:

• Windows builds still expect mingw-w64.
• macOS-to-Linux builds use cargo zigbuild when available.
• Native macOS builds use the platform default linker when you run cargo +nightly build --profile=release.
• Linux-to-macOS cross-builds expect osxcross to provide binaries such as x86_64-apple-darwin23-clang.
• If cargo zigbuild is installed, the build script will use it automatically.
• make install_cross is now the portable entry point and delegates to scripts/install-cross.sh.