Install arachne
With conda:
This assumes an environment has already been created with conda create
for
mamba: just swapcondawithmamba
conda install -c bioconda -c conda-forge bioconda::arachneWith pixi
This assumes a pixi project was already created with pixi init and has the conda-forge and bioconda channels added
pixi add arachneManually Compile
git clone --recursive https://github.com/pdimens/arachne.gitThe inclusion of --recursive is important to make sure the minibwa dependency is cloned as well.
Direct compilation requires a few dependencies in your software environment:
- Go
- a C compiler and zlib
- a CPU with SSE4.2 (x86-64) or NEON (arm64), which minibwa requires
- optionally OpenMP (
libgomp), used byarachne indexfor multi-threaded index construction. It is detected automatically when building; without it indexing is single-threaded
cd arachne
make clean; makeFor development portability, Arachne also provides a pixi environment with the build dependencies. Once arachne is compiled, the pixi environment is no longer needed. This approach assumes pixi is installed in your software environment. To use the pixi approach:
cd arachne
pixi run buildThis results in the compiled executable binaries bin/arachne and bin/minibwa. You can use them there
or copy them into another path.