61 lines
1.5 KiB
Markdown
61 lines
1.5 KiB
Markdown
# Alphafold
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Alphafold contains two parts:
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1. A conda environment containing dependencies
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2. The alphafold module itself, containing the current code and submission scripts.
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## Conda Environment
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Alphafold was installed based on Dima's instructions on ra
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(`/das/work/common/opt/alphafold/2021-07/INSTALL`).
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On pmod6 as an admin user:
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```
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conda create --name alphafold python==3.8
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conda update -n base conda
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source miniconda3/etc/profile.d/conda.sh
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conda activate alphafold
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conda install -y -c conda-forge openmm==7.5.1 cudnn==8.2.1.32 cudatoolkit==11.0.3 pdbfixer==1.7
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conda install -y -c bioconda hmmer==3.3.2 hhsuite==3.3.0 kalign2==2.04
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pip install absl-py==0.13.0 biopython==1.79 chex==0.0.7 dm-haiku==0.0.4 \
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dm-tree==0.1.6 immutabledict==2.0.0 jax==0.2.14 ml-collections==0.1.0 \
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numpy==1.19.5 scipy==1.7.0 tensorflow==2.5.0 pandas==1.3.4
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pip install --upgrade jax jaxlib==0.1.69+cuda111 \
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-f https://storage.googleapis.com/jax-releases/jax_releases.html
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```
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If this needs to be updated in the future we may need to have versioned conda envs.
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## Alphafold module
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Add version to files/variants. The version number should match a github tag
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(e.g. `v2.0.1`) or else have the commit hash as `$V_RELEASE`.
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As admin user:
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```
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cd MX/alphafold
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./build <version>
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```
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## Testing
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Here's an example sequence:
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```
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mkdir example
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cd example
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cat > query.fasta <<EOF
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>dummy_sequence
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GWSTELEKHREELKEFLKKEGITNVEIRIDNGRLEVRVEGGTERLKRFLEELRQKLEKKGYTVDIKIE
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EOF
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module use MX unstable
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module load alphafold/2.1.1
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sbatch alphafold_merlin.sh query.fasta
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```
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