Merge branch 'alphafold' into 'master'

Alphafold buildblock See merge request Pmodules/buildblocks!228
2021-10-27 07:26:16 +00:00
parent a1ddb7afd4 5233ffd6e6
commit 2dc5098d35
8 changed files with 265 additions and 0 deletions
--- a/MX/alphafold/README.md
+++ b/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
+```
+
--- a/MX/alphafold/bin/submit.sh
+++ b/MX/alphafold/bin/submit.sh
@@ -0,0 +1,91 @@
+#!/bin/bash
+
+# Generic alphafold submission script.
+# Set the ALPHAFOLD_DATA variable before running.
+# Usage: sbatch [slurm_opts] $ALPHAFOLD_DIR/bin/submit.sh fasta_file [max_template_date]
+#
+# Output will be in the same directory as the fasta_file.
+# Slurm logs will be in the current directory.
+#
+# 2021-08-09 Spencer Bliven, D.Ozerov
+#
+
+# Bash strict mode
+set -euo pipefail
+IFS=$'\n\t'
+
+usage () {
+    echo "Usage: sbatch [slurm_opts] \$ALPHAFOLD_DIR/bin/submit_merlin.sh fasta_file [max_template_date]"
+}
+
+# Parse parameters
+if [ "$#" -lt 1 ]
+then
+    echo "No fasta_file name" >&2
+    usage >&2
+    exit
+fi
+
+FASTA_FILE=`readlink -f $1`
+if [ ! -e ${FASTA_FILE} ] || [ "$FASTA_FILE" == "" ]
+then
+    echo "${FASTA_FILE} is not reachable (input argument was $1)"
+    exit
+fi
+
+DIR_QUERY=`dirname ${FASTA_FILE}`
+LOG="${DIR_QUERY}/alphafold.out"
+
+if [ "$#" -ge 2 ]
+then
+    MAX_TEMPLATE_DATE=$2
+else
+    MAX_TEMPLATE_DATE=$(date '+%Y-%m-%d')
+fi
+
+date     > "$LOG"
+hostname >> "$LOG"
+
+set +u # Allow unset variables in activate commands
+module purge
+module use MX unstable
+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
+
+# Check the module loaded correctly
+if ! [ -d "${ALPHAFOLD_HOME}" ]; then
+    echo "Error: $ALPHAFOLD_HOME not available" >&2
+    exit 1
+fi
+
+# Data dir
+if ! [ -d "${ALPHAFOLD_DATA:?Set ALPHAFOLD_DATA before running}" ]; then
+    echo "Error: ALPHAFOLD_DATA directory not available ($ALPHAFOLD_DATA)" >&2
+    exit 1
+fi
+
+echo "GPUs: ${CUDA_VISIBLE_DEVICES:-None}" >> "$LOG"
+echo "Detecting GPUs with Tensorflow:" >> "$LOG"
+python -c 'import tensorflow as tf; tf.compat.v1.Session(config=tf.compat.v1.ConfigProto(log_device_placement=True))' 2>&1 |
+    sed -rn 's/^.* (Created TensorFlow device.*)$/\1/p' >> "$LOG"
+echo >> "$LOG"
+
+echo "Running alphafold from $PWD for fasta sequence : " >> "$LOG"
+cat ${FASTA_FILE} >> "$LOG"
+echo "and max_template_date : ${MAX_TEMPLATE_DATE} " >> "$LOG"
+echo >> "$LOG"
+
+
+cd "${ALPHAFOLD_HOME}"
+CMD=("./run_alphafold.sh" -p full_dbs -d "${ALPHAFOLD_DATA}" -o "${DIR_QUERY}" -m model_1,model_2,model_3,model_4,model_5 -f "${FASTA_FILE}" -t "${MAX_TEMPLATE_DATE}")
+if [ -z "${CUDA_VISIBLE_DEVICES:-}" ]
+then
+    CMD+=(-g false)
+else
+    CMD+=(-a "$CUDA_VISIBLE_DEVICES")
+fi
+
+echo "Run: ${CMD[@]}" >> "$LOG"
+echo >> "$LOG"
+( ( time "${CMD[@]}" ) 2>&1 ) >> "$LOG"
--- a/MX/alphafold/bin/submit_merlin.sh
+++ b/MX/alphafold/bin/submit_merlin.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+#SBATCH -p gpu
+#SBATCH -J alphafold
+#SBATCH -M gmerlin6
+#SBATCH --gpus=1
+#SBATCH -n 1
+#SBATCH -c 10
+
+# Alphafold submission script for the merlin cluster
+# Usage: sbatch [slurm_opts] $ALPHAFOLD_DIR/bin/submit_merlin.sh fasta_file [max_template_date]
+#
+# Output will be in the same directory as the fasta_file.
+# Slurm logs will be in the current directory.
+#
+# 2021-08-09 Spencer Bliven, D.Ozerov
+#
+
+export ALPHAFOLD_DATA=/data/project/bio/shared/alphafold
+module purge
+module use MX unstable
+module load alphafold/ALPHAFOLD_VERSION
+
+exec "${ALPHAFOLD_DIR:?Error loading module}/bin/submit.sh" "$@"
--- a/MX/alphafold/bin/submit_ra.sh
+++ b/MX/alphafold/bin/submit_ra.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+#SBATCH -p day
+#SBATCH -t 1-00:00:00
+#SBATCH -J alphafold
+#SBATCH -n 1
+#SBATCH -c 10
+
+# Alphafold submission script for the ra cluster
+# Usage: sbatch [slurm_opts] $ALPHAFOLD_DIR/bin/submit_merlin.sh fasta_file [max_template_date]
+#
+# Output will be in the same directory as the fasta_file.
+# Slurm logs will be in the current directory.
+#
+# 2021-08-09 Spencer Bliven, D.Ozerov
+#
+
+export ALPHAFOLD_DATA=/das/work/common/opt/alphafold/data
+
+# Need at least rc6 to see alphafold
+PMODULES_VERSION=1.0.0rc10;
+source /opt/psi/config/profile.bash;
+
+module --version
+
+module purge
+module use MX unstable Programming
+module load alphafold/ALPHAFOLD_VERSION
+module list
+
+exec "${ALPHAFOLD_DIR:?Error loading module}/bin/submit.sh" "$@"
--- a/MX/alphafold/build
+++ b/MX/alphafold/build
@@ -0,0 +1,42 @@
+#!/usr/bin/env modbuild
+
+pbuild::add_to_group 'MX'
+
+
+pbuild::prep() {
+    :
+}
+
+pbuild::configure() {
+    :
+}
+
+pbuild::compile() {
+    :
+}
+
+pbuild::install() {
+    ALPHAFOLD_HOME="$PREFIX/alphafold"
+
+    local BRANCH
+    if [[ "${#V_RELEASE}" -eq 7 ]]; then
+        # Release looks like a git hash
+        BRANCH="${V_RELEASE}"
+    else
+        BRANCH="v${V_PKG}"
+    fi
+
+    git clone --depth=1 -b "$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" "$PREFIX/bin/"*
+}
+
--- a/MX/alphafold/files/variants
+++ b/MX/alphafold/files/variants
@@ -0,0 +1,2 @@
+alphafold/2.0.0-b88f8da	unstable	anaconda/2019.07 b:gcc/10.3.0 cuda/11.0.3
+alphafold/2.0.1	unstable	anaconda/2019.07 b:gcc/10.3.0 cuda/11.0.3
--- a/MX/alphafold/modulefile
+++ b/MX/alphafold/modulefile
@@ -0,0 +1,15 @@
+#%Module1.0
+
+module-whatis	        "AlphaFold"
+module-url		"https://github.com/deepmind/alphafold/"
+module-license	        "Code: Apache 2.0 License. Parameters: Noncommercial CC-BY-NC 4.0"
+module-maintainer	"Spencer Bliven <spencer.bliven@psi.ch"
+
+module-help	"The AlphaFold 2 protein structure prediction method by Google DeepMind.
+
+Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021). https://doi.org/10.1038/s41586-021-03819-2
+"
+
+setenv ALPHAFOLD_HOME "$PREFIX/alphafold"
+setenv ALPHAFOLD_ENV "alphafold"
+
--- a/Programming/anaconda/2019.07/conda-env-defs/alphafold/README
+++ b/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.