Installation

Simpleaf can be installed from source, from crates.io, or installed via bioconda. simpleaf requires alevin-fry, piscem, and wget.

Caution

This release requires piscem >= 0.22.0 and alevin-fry >= 0.17.0. These are hard requirements, not recommendations: simpleaf set-paths will reject older binaries. piscem 0.22.0 changed the meaning of -t (see Threads and decompression) and added the build options simpleaf now passes unconditionally, so an older piscem cannot run these commands. If you install from bioconda, check that the versions it resolves meet these floors.

Recommended: installing from conda

We recommend that Linux and macOS users install simpleaf from bioconda, because all its dependencies are also available on conda, and will be automatically installed (except piscem) when installing simpleaf.

conda install simpleaf piscem -c bioconda -c conda-forge

Apple-silicon and ARM users need no special handling. bioconda ships native osx-arm64 and linux-aarch64 packages for simpleaf, piscem, and alevin-fry, so the command above works as-is in a native shell. Rosetta2 is not required, and installing under emulation is no longer recommended.

Installing with cargo

cargo is the rust package manager. simpleaf is available on crate.io and can be installed from cargo.

cargo install simpleaf

Once installed, one will need to set the path to the executable of dependencies using the simpleaf set-paths program as discussed in section Set Up Simpleaf manually.

Building from source (from GitHub)

You can also choose to build simpleaf from source by pulling its GitHub repo and build it as a normal rust program. Then, one needs to set up simpleaf manually.

git clone https://github.com/COMBINE-lab/simpleaf.git && cd simpleaf
cargo build --release