Installation¶

From source¶

Rust 1.95 or later. From a clone of rnabioco/eschalign:

cargo build --release                                   # target/release/eschalign
cargo build --release --features gpu -p eschalign-cli   # with the CUDA score kernel

Local builds pin -C target-cpu=x86-64-v3 (.cargo/config.toml); the AVX-512 kernels are chosen at run time. Do not use target-cpu=native: see Development.

On a cluster¶

Use the pixi environments, which provide the mold linker, samtools, cargo-nextest and the CUDA runtime. Do not build on a login node:

srun -p rna -c 32 --mem=32G pixi run -e dev build-rel

See Development for the Beevol and Alpine srun forms.

GPU runtime¶

Nothing CUDA is needed to build. For the run-time environment see GPU.

First run¶

eschalign reads.ubam -r trna.fa -o aligned.bam

Options and output are documented under Usage.