colabfold_v1_3_0.def

Bootstrap: docker
From: nvidia/cuda:11.1.1-cudnn8-runtime-ubuntu20.04

%setup
#section are first executed on the host system outside of the container after the base OS has been installed. . You can reference the container file system with the $SINGULARITY_ROOTFS environment variable in the %setup section


%files
#The %files section allows you to copy files into the container with greater safety than using the %setup section. Its general form is
#Useless for now.

%environment
  #Define environment variable that will be executed at each runtime.
  export TF_FORCE_UNIFIED_MEMORY=1
  export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0
  export OPENMM_CPU_THREADS=32
  export CUDA=11.1
  export PATH=/opt/MMseqs2/build/bin/:$PATH

  #PATH
  export PATH=/usr/local/cuda-11.1/bin:$PATH
  export LD_LIBRARY_PATH=/usr/local/cuda-11.1/lib64:$LD_LIBRARY_PATH
  export PATH=/opt/conda/bin:$PATH
  export XDG_CACHE_HOME=/opt/cache
  export COLABFOLDDIR=/opt/conda/lib/python3.7/site-packages/colabfold


%post -c /bin/bash

  #Redefine the variables
  export CUDA=11.1
  export XDG_CACHE_HOME=/opt/cache
  export COLABFOLDDIR=/opt/conda/lib/python3.7/site-packages/colabfold


  #Install necessary packages
  echo "
  
  =======STARTING APT INSTALL=======
  
  "
  apt-get update
  DEBIAN_FRONTEND=noninteractive apt-get install -y \
        build-essential \
        tzdata \
        cuda-command-line-tools-${CUDA/./-} 

  echo "
  
  =======STARTING INSTALL 2=======
  
  "  is:issue is:open 
  apt-get update
  DEBIAN_FRONTEND=noninteractive apt-get install -y \
        cmake \
        hmmer \
        kalign \
        wget \
        curl \
        vim \
        nano \
        git \
        gcc \
        mpi \
        openmpi-bin \
        openmpi-common \
        libopenmpi-dev \
        libgtk2.0-dev \
        libfontconfig1-dev \
        libfreetype6-dev \
        libfreetype6 
  rm -Rf /var/lib/apt/lists/*

  echo "
  
  =======INSTALLING MMSEQS2=======
  
  "

  # Install MMSEQS - using the latest verified version on github (master commit a5d49655330d144788c6e1bf8551d7cc1d356b0c 23 Jan 2023)
  cd  /opt && \
  git clone https://github.com/soedinglab/MMseqs2.git && \
  cd MMseqs2 && \
  git checkout a5d49655330d144788c6e1bf8551d7cc1d356b0c && \
  mkdir build && \
  cd build && \
  cmake -DCMAKE_BUILD_TYPE=RELEASE -DHAVE_MPI=1 -DCMAKE_INSTALL_PREFIX=. -DHAVE_AVX2=1 .. && \
  make && \
  make install && \
  export PATH=/opt/MMseqs2/build/bin/:$PATH

  echo "
  
  =======INSTALLING MINICONDA=======
  
  "

  # Install Miniconda package manager
  wget -q -P /tmp \
    https://repo.anaconda.com/miniconda/Miniconda3-py37_4.9.2-Linux-x86_64.sh \
      && bash /tmp/Miniconda3-py37_4.9.2-Linux-x86_64.sh -b -p /opt/conda \
      && rm /tmp/Miniconda3-py37_4.9.2-Linux-x86_64.sh
  export PATH=/opt/conda/bin:$PATH

  echo "
  
  =======INSTALLING OPENMM/PDBFIXER=======
  
  "

  # Install necessary soft with conda
  conda update -qy conda \
      && conda install -y -c conda-forge \
        openmm=7.5.1 \
        pdbfixer \
        pip \
        #cudatoolkit==${CUDA} \

  echo "
  
  =======INSTALLING ALIGNMENT TOOLS=======
  
  "

  # Install alignment tools
  conda install -c conda-forge -c bioconda kalign3=3.2.2 hhsuite=3.3.0 -y

  echo "
  
  =======INSTALLING COLABFOLD=======
  
  "

  # Install ColabFold (latest verified version on github commit 38e21e3 on 23 Jan 2023) and Jaxlib
  conda config --set ssl_verify no
  python -m pip install --default-timeout=300 --no-warn-conflicts "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold@38e21e30f44df8a7a3aa6b8ddc0c4a4826b43e1a"
  python -m pip install --default-timeout=300 https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.15+cuda11.cudnn82-cp37-none-manylinux2014_x86_64.whl
  python -m pip install --default-timeout=300 jax==0.3.15
  # add permissions to libs in case it's not already done as it may cause a few weird error messages later on
  chmod g+w -R /opt/conda/lib/python3.7/site-packages/
  chmod a+xr -R /opt/conda/lib/python3.7/site-packages/

  echo "
  
  =======RUNNING PATCHES=======
  
  "

  # Patch Colabfold batch.py to remove environment variable for GPU memory. Those variable are set up externally
  # Colabfold v1.3.0 March 2022 doesnt have random seed, those changes come about later on in Oct 2022 but arent integrated in a stable release yet.
  cd /opt/conda/lib/python3.7/site-packages/colabfold/ && \
  echo '--- batch.py
+++ batch.py
@@ -2,8 +2,8 @@ from __future__ import annotations
 
 import os
 
-os.environ["TF_FORCE_UNIFIED_MEMORY"] = "1"
-os.environ["XLA_PYTHON_CLIENT_MEM_FRACTION"] = "2.0"
+# os.environ["TF_FORCE_UNIFIED_MEMORY"] = "1"
+# os.environ["XLA_PYTHON_CLIENT_MEM_FRACTION"] = "2.0"
 
 import json
 import logging
@@ -1745,7 +1745,7 @@ def main():
             f"--max-msa can not be used in combination with AlphaFold2-multimer (--max-msa ignored)"
         )
         args.max_msa = None
-    download_alphafold_params(model_type, data_dir)
+    data_dir = download_alphafold_params(model_type, data_dir)
     uses_api = any((query[2] is None for query in queries))
     if uses_api and args.host_url == DEFAULT_API_SERVER:
         print(ACCEPT_DEFAULT_TERMS, file=sys.stderr)
' > add_predefined_params_folder.patch && \
  patch -p0 -N -f -s -i add_predefined_params_folder.patch && \
  rm add_predefined_params_folder.patch 

  cd /opt/conda/lib/python3.7/site-packages/colabfold/ && \
  echo '--- download.py
+++ download.py
@@ -1,7 +1,7 @@
 import logging
 import tarfile
 from pathlib import Path
-
+import os
 import appdirs
 import tqdm
 
@@ -9,29 +9,35 @@ logger = logging.getLogger(__name__)
 
 # The data dir location logic switches between a version with and one without "params" because alphafold
 # always internally joins "params". (We should probably patch alphafold)
-default_data_dir = Path(appdirs.user_cache_dir(__package__ or "colabfold"))
+# default_data_dir = Path(appdirs.user_cache_dir(__package__ or "colabfold"))
+default_data_dir = Path(os.environ["TMPDIR"])
 
 
 def download_alphafold_params(model_type: str, data_dir: Path = default_data_dir):
     import requests
 
-    params_dir = data_dir.joinpath("params")
     if model_type == "AlphaFold2-multimer-v2":
         url = "https://storage.googleapis.com/alphafold/alphafold_params_colab_2022-03-02.tar"
+        data_dir = data_dir.joinpath("complexes_multimer-v2")
+        params_dir = data_dir.joinpath("params")
         success_marker = params_dir.joinpath(
             "download_complexes_multimer-v2_finished.txt"
         )
     elif model_type == "AlphaFold2-multimer-v1":
         url = "https://storage.googleapis.com/alphafold/alphafold_params_colab_2021-10-27.tar"
+        data_dir = data_dir.joinpath("complexes_multimer-v1")
+        params_dir = data_dir.joinpath("params")
         success_marker = params_dir.joinpath(
             "download_complexes_multimer-v1_finished.txt"
         )
     else:
         url = "https://storage.googleapis.com/alphafold/alphafold_params_2021-07-14.tar"
+        data_dir = data_dir.joinpath("monomere")
+        params_dir = data_dir.joinpath("params")
         success_marker = params_dir.joinpath("download_finished.txt")
 
     if success_marker.is_file():
-        return
+        return data_dir
 
     params_dir.mkdir(parents=True, exist_ok=True)
     response = requests.get(url, stream=True)
@@ -47,6 +53,7 @@ def download_alphafold_params(model_type: str, data_dir: Path = default_data_dir
         file.extractall(path=params_dir)
     success_marker.touch()
 
+    return data_dir
 
 if __name__ == "__main__":
     # TODO: Arg to select which one
' > change_tmpdir_download.patch && \
  patch -p0 -N -f -s -i change_tmpdir_download.patch && \
  rm change_tmpdir_download.patch

  # #Apply patches and parameters
  # cd $COLABFOLDDIR
  # sed -i -e "s#props_path = \"stereo_chemical_props.txt\"#props_path = \"${COLABFOLDDIR}/stereo_chemical_props.txt\"#" batch.py
  # wget -q https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
  # wget https://raw.githubusercontent.com/deepmind/alphafold/main/docker/openmm.patch
  # (cd  /opt/conda/lib/python3.7/site-packages; wget https://raw.githubusercontent.com/deepmind/alphafold/main/docker/openmm.patch; patch -s -p0 < openmm.patch; rm openmm.patch)
  # (cd  /opt/conda/lib/python3.7/site-packages/colabfold/; wget https://raw.githubusercontent.com/tubiana/colabfold_singularity/main/matplotlib.patch; patch -s -p0 < matplotlib.patch; rm matplotlib.patch)

%labels
  author Thibault Tubiana [Chloe Quignot: mmseqs installation via git (latest verified release version a5d4965) + colabfold defined to latest verified release (master branch commit 38e21e3)] 


%help
  Singularity for running colabfold localy. 
  NOTE :
   - databases like Uniref30 or other are too big to be placed in the container. Therefore your need to download them and place them outside (check https://colabfold.mmseqs.com). Give this folder later to the picture (see usage).
   - alphafold parameters are downloaded outsite of the container as well. You will need to give a specific folder for that as well.
  
  USAGE:
   1. Define location folder of 
      - DATABASES: Root folder that the database (should have "uniref30" inside etc..)
      - PARAMS_DIR: fodler that will contain Alphafold Cache File, corresponds to XDG_CACHE_HOME

   2. You can setup a shortcut for the singularity container with:
      SINGULARITYCOMAND="singularity exec \
      -B $PWD,${DATABASES},${PARAMS_DIR}:/opt/cache/colabfold \
      --nv ${IMAGESINGULARITY}"

  3. Run colabfold_batch and colabfold_search with command like :
  CUDA_VISIBLE_DEVICES=0 $SINGULARITYCOMAND colabfold_batch your_msa.a3m your_outdir/