Installation#
Simpleaf can be installed from source, from crates.io, or installed via bioconda. simpleaf alevin-fry, and either piscem or salmon (or both if you prefer), as well as wget.
Recommended: installing from conda#
We recommend all x86 (Linux or Mac) users to 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
For Apple-silicon computers, for example those with an Apple M-series chip, simpleaf should be installed under the x86 emulation layer, in other words, in shell with Rosetta2 enabled. See this for details. Furthermore, if one would like to use piscem on apple silicon, one has to either download the pre-built piscem executable or build piscem from source in the native shell (with Rosetta2 disabled) using the commands described here. Then, piscem can be executed from both Rosetta2 enabled and disabled shell.
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