Installation

Requirements

Exact requirements may vary depending on what channels are used to install the tools.

• Rust compiler, [https://rust-lang.org/learn/get-started/].
• C++ compiler
• git
• conda

How-to

msweep-rs

From source:

git clone https://codeberg.org/themaklin/msweep-rs
cd msweep-rs
git clone https://github.com/tmaklin/sketchlib.rust vendor/sketchlib.rust -b no-panic-from-rollhash-set_k
git clone https://github.com/tmaklin/sparrowhawk vendor/sparrowhawk -b assembly-api
cd vendor/sketchlib.rust
git apply ../../patches/sketchlib.patch
cd ../../
cd vendor/sparrowhawk
git apply ../../patches/sparrowhawk.patch
cd ../../
cargo build --release

ahda

From crates.io:

cargo install ahda

From source:

git clone https://codeberg.org/themaklin/ahda -b v0.1.1
cd ahda
cargo build --release

Pseudoaligners

Themisto

Download a precompiled binary from GitHub or see https://github.com/algbio/themisto for other options.

Fulgor

Install from bioconda or see https://github.com/jermp/fulgor for other options.

PopPUNK

Install from bioconda or see https://github.com/bacpop/poppunk for other options.