diff --git a/README.md b/README.md index 7de2e87..1f81352 100644 --- a/README.md +++ b/README.md @@ -33,12 +33,25 @@ conda install -c bioconda anglerfish pip install --upgrade --force-reinstall git+https://github.com/remiolsen/anglerfish.git ``` +### For Arm64 processors (e.g. Apple M2) + +Anglerfish depends on minimap2 which needs to be [compiled from source](https://github.com/lh3/minimap2?tab=readme-ov-file#installation) for Arm64 processors. +When minimap2 is compiled and available on $PATH, anglerfish can be installed with pip: + +```shell +pip install bio-anglerfish +``` + +The Dockerfile supplied here includes a + ## Source development 1. [Install miniconda](https://docs.conda.io/en/latest/miniconda.html). 2. Set up repo clone with editable install +For x86 processors (e.g. Intle/AMD): + ``` git clone https://github.com/remiolsen/anglerfish.git cd anglerfish @@ -49,6 +62,18 @@ conda activate anglerfish-dev pip install -e ".[dev]" ``` +For Arm64 processors (e.g. Apple M1/M2). First [compile and install minimap2 manually](https://github.com/lh3/minimap2?tab=readme-ov-file#installation), then: + +``` +git clone https://github.com/remiolsen/anglerfish.git +cd anglerfish +# Create a the anglerfish conda environment (but remove minimap2) +conda env create -f <(grep -v minimap2 environment.yml) +# Install anglerfish +conda activate anglerfish-dev +pip install -e ".[dev]" +``` + 3. (Optional) Install pre-commit to prevent committing code that will fail linting ```