AlphaFold containers to run on the Artemis HPC (Centos 6.10, cuda/10.2.89)
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Each container has an ubuntu 16.04 base with cuda 10.2.89 installed. This is the Singularity versions will work on a CentOS 6.10 host (glibc 2.17). These seem to be the highest version of AlphaFold that can be used with cuda 10.2 (jaxlib-0.1.71+cuda102 and jax 0.2.25).
See the AlphaFold training repo for more details: https://github.com/Sydney-Informatics-Hub/training.alphafold/tree/main/docker
Build with:
sudo docker build -t sydneyinformaticshub/alphafold:colabfold_v1.3.0 .
Push with:
sudo docker push sydneyinformaticshub/alphafold:colabfold_v1.3.0
Run with:
sudo docker run -it --gpus=all sydneyinformaticshub/alphafold:colabfold_v1.3.0 /bin/bash -c "colabfold_batch --amber --templates --num-recycle 1 input.fasta output_dir/
Set your directories
export SINGULARITY_CACHEDIR=`pwd`
export SINGULARITY_TMPDIR=`pwd`
Build:
singularity build colab.img docker://sydneyinformaticshub/alphafold:colabfold_v1.3.0
Run:
singularity run --nv colab.img /bin/bash -c "colabfold_batch --amber --templates --num-recycle 1 input.fasta output_dir/"
Content type
Image
Digest
sha256:f52930380…
Size
7.9 GB
Last updated
about 3 years ago
docker pull sydneyinformaticshub/alphafold:alphafold_v2.2.3