Release Alphafold 2.0.1

- Improves the build system to install the submission scripts in bin
- Add README

MX/alphafold/README.md

@@ -0,0 +1,60 @@
+# Alphafold
+
+Alphafold contains two parts:
+1. A conda environment containing dependencies
+2. The alphafold module itself, containing the current code and submission scripts.
+
+## Conda Environment
+
+Alphafold was installed based on Dima's instructions on ra
+(`/das/work/common/opt/alphafold/2021-07/INSTALL`).
+
+On pmod6 as an admin user:
+
+```
+conda create --name alphafold python==3.8
+conda update -n base conda
+
+source miniconda3/etc/profile.d/conda.sh
+conda activate alphafold
+
+conda install -y -c conda-forge openmm==7.5.1 cudnn==8.2.1.32 cudatoolkit==11.0.3 pdbfixer==1.7
+conda install -y -c bioconda hmmer==3.3.2 hhsuite==3.3.0 kalign2==2.04
+
+pip install absl-py==0.13.0 biopython==1.79 chex==0.0.7 dm-haiku==0.0.4 \
+    dm-tree==0.1.6 immutabledict==2.0.0 jax==0.2.14 ml-collections==0.1.0 \
+    numpy==1.19.5 scipy==1.7.0 tensorflow==2.5.0
+pip install --upgrade jax jaxlib==0.1.69+cuda111 \
+    -f https://storage.googleapis.com/jax-releases/jax_releases.html
+```
+
+If this needs to be updated in the future we may need to have versioned conda envs.
+
+## Alphafold module
+
+Add version to files/variants. The version number should match a github tag
+(e.g. `v2.0.1`) or else have the commit hash as `$V_RELEASE`.
+
+As admin user:
+```
+cd MX/alphafold
+./build <version>
+```
+
+## Testing
+
+Here's an example sequence:
+
+```
+mkdir example
+cd example
+cat > query.fasta <<EOF
+>dummy_sequence
+GWSTELEKHREELKEFLKKEGITNVEIRIDNGRLEVRVEGGTERLKRFLEELRQKLEKKGYTVDIKIE
+EOF
+
+module use MX unstable
+module load alphafold/2.0.1
+sbatch $ALPHAFOLD_DIR/bin/submit_merlin.sh query.fasta
+```
+

MX/alphafold/bin/submit.sh

@@ -49,7 +49,7 @@ hostname >> "$LOG"
 set +u # Allow unset variables in activate commands
 module purge
 module use MX unstable
-module load anaconda/2019.07 cuda/11.0.3 alphafold/2.0.0-b88f8da 2>> "$LOG"
+module load alphafold/ALPHAFOLD_VERSION 2>> "$LOG"
 conda activate "${ALPHAFOLD_ENV:?"Error: ALPHAFOLD_ENV not set. Try 'module use MX unstable; module load alphafold'"}"
 set -u
 

MX/alphafold/bin/submit_merlin.sh

@@ -18,6 +18,6 @@
 export ALPHAFOLD_DATA=/data/project/bio/shared/alphafold
 module purge
 module use MX unstable
-module load anaconda/2019.07 cuda/11.0.3 alphafold/2.0.0-b88f8da
+module load alphafold/ALPHAFOLD_VERSION
 
 exec "${ALPHAFOLD_DIR:?Error loading module}/bin/submit.sh" "$@"

MX/alphafold/bin/submit_ra.sh

@@ -24,7 +24,7 @@ module --version
 
 module purge
 module use MX unstable Programming
-module load anaconda/2019.07 cuda/11.0.3 alphafold/2.0.0-b88f8da
+module load alphafold/ALPHAFOLD_VERSION
 module list
 
 exec "${ALPHAFOLD_DIR:?Error loading module}/bin/submit.sh" "$@"

MX/alphafold/build

@@ -29,9 +29,14 @@ pbuild::install() {
     git clone --depth=1 -b "$BRANCH" https://github.com/deepmind/alphafold.git "$ALPHAFOLD_HOME" || return $?
     if ! [ -f "$ALPHAFOLD_HOME/alphafold/common/stereo_chemical_props.txt" ]; then
         wget -q -P "$ALPHAFOLD_HOME/alphafold/common/" \
+            --no-check-certificate `# wget root certs are old` \
             https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
     fi
     wget -O "$ALPHAFOLD_HOME/run_alphafold.sh" \
         https://raw.githubusercontent.com/kalininalab/alphafold_non_docker/main/run_alphafold.sh
     chmod +x "$ALPHAFOLD_HOME/run_alphafold.sh"
+
+    cp -r "$BUILDBLOCK_DIR/bin" "$PREFIX/"
+    sed -i "s/ALPHAFOLD_VERSION/$V/g" "$PREFIX/bin/"*
 }
+

MX/alphafold/files/variants

@@ -1 +1,2 @@
-alphafold/2.0.0-b88f8da	anaconda/2019.07 b:gcc/10.3.0 cuda/11.0.3
+alphafold/2.0.0-b88f8da	unstable	anaconda/2019.07 b:gcc/10.3.0 cuda/11.0.3
+alphafold/2.0.1	unstable	anaconda/2019.07 b:gcc/10.3.0 cuda/11.0.3

Programming/anaconda/2019.07/conda-env-defs/alphafold/README

@@ -0,0 +1,2 @@
+The alphafold environment is a complex mixture of conda and pip. See
+MX/alphafold/README.md.