Attention

These docs have moved. The current simpleaf documentation lives at https://combine-lab.github.io/simpleaf and is the only version that is updated. This readthedocs site is a frozen snapshot of the 0.27.0 docs and will not track later releases.

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 >= 0.24.0 and alevin-fry >= 0.19.0. These are hard requirements, not recommendations: simpleaf set-paths will reject older binaries, and quant, multiplex-quant and atac process re-check both registered tools (index and atac index re-check piscem) before any work. Upgrade the two together: piscem 0.24.0 writes RAD v2, which alevin-fry 0.18.x cannot read (its generate-permit-list aborts with an “invalid utf-8 sequence” panic), while alevin-fry 0.19.0 reads both RAD v2 and the RAD v1 written by earlier piscem, including mapped directories passed with --map-dir. piscem 0.24.0 also changes the index format, so indexes built with an earlier piscem must be rebuilt with simpleaf index; piscem stops on an old index with a “must be rebuilt” error. Flex probe indexes that multiplex-quant cached itself under $ALEVIN_FRY_HOME/probe_indices are rebuilt automatically on first use; delete that directory only if the cache is read-only to you. 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