Pre-built images are available on Docker Hub. The image bundles the slorado binary (on PATH, at /slorado/bin) along with the well tested models under /slorado/models.
The image also bundles blue-crab and slow5tools.
Builds for both AMD (rocm) and NVIDIA (cuda) are available.
docker pull hasindu2008/slorado:0.6.0-rocm
Print the help message to check the image works:
docker run --rm hasindu2008/slorado:0.6.0-rocm slorado basecaller --help
To basecall on an AMD GPU, expose the GPU devices to the container and bind mount the directory holding your BLOW5 file:
docker run -v "$PWD":/data \
--device=/dev/kfd --device=/dev/dri \
--security-opt seccomp=unconfined --group-add video \
hasindu2008/slorado:0.6.0-rocm \
slorado basecaller /slorado/models/dna_r10.4.1_e8.2_400bps_hac@v5.0.0 /data/reads.blow5 -o /data/reads.fastq -x cuda:all
Note that -x cuda:all selects all GPUs for the rocm build too. If --group-add video fails with Unable to find group video, pass the numeric gid instead ($(getent group video | cut -d: -f3)).
docker pull hasindu2008/slorado:0.6.0-cuda
Print the help message to check the image works:
docker run --rm hasindu2008/slorado:0.6.0-cuda slorado basecaller --help
To basecall on an NVIDIA GPU, expose the GPU devices to the container and bind mount the directory holding your BLOW5 file:
docker run -v "$PWD":/data --gpus all \
hasindu2008/slorado:0.6.0-cuda \
slorado basecaller /slorado/models/dna_r10.4.1_e8.2_400bps_hac@v5.0.0 /data/reads.blow5 -o /data/reads.fastq -x cuda:all