Please install tensorflow v2.3.* before installing deepchem.
pip install tensorflow==2.3.*
Then, you install deepchem via pip or conda.
pip install deepchem
conda install -c conda-forge deepchem
RDKit is a soft requirement package, but many useful methods like molnet depend on it. We recommend installing RDKit with deepchem if you use conda.
conda install -y -c conda-forge rdkit
Nightly build version¶
You install the nightly build version via pip. The nightly version is built by the HEAD of DeepChem.
pip install tensorflow==2.3.* pip install --pre deepchem
If you want to install using a docker, you can pull two kinds of images from DockerHub.
Image built by using a conda (x.x.x is a version of deepchem)
This image is built when we push x.x.x. tag
Dockerfile is put in `docker/tag`_ directory
Image built from source codes
This image is built every time we commit to the master branch
Dockerfile is put in `docker/nightly`_ directory
First, you pull the image you want to use.
docker pull deepchemio/deepchem:latest
Then, you create a container based on the image.
docker run --rm -it deepchemio/deepchem:latest
If you want GPU support:
# If nvidia-docker is installed nvidia-docker run --rm -it deepchemio/deepchem:latest docker run --runtime nvidia --rm -it deepchemio/deepchem:latest # If nvidia-container-toolkit is installed docker run --gpus all --rm -it deepchemio/deepchem:latest
You are now in a docker container which deepchem was installed. You can start playing with it in the command line.
(deepchem) root@xxxxxxxxxxxxx:~/mydir# python Python 3.6.10 |Anaconda, Inc.| (default, May 8 2020, 02:54:21) [GCC 7.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import deepchem as dc
If you want to check the tox21 benchmark:
# you can run our tox21 benchmark (deepchem) root@xxxxxxxxxxxxx:~/mydir# wget https://raw.githubusercontent.com/deepchem/deepchem/master/examples/benchmark.py (deepchem) root@xxxxxxxxxxxxx:~/mydir# python benchmark.py -d tox21 -m graphconv -s random
From source with conda¶
Installing via these steps will ensure you are installing from the source.
Shell: Bash, Zsh, PowerShell
First, please clone the deepchem repository from GitHub.
git clone https://github.com/deepchem/deepchem.git cd deepchem
Then, execute the shell script. The shell scripts require two arguments, python version and gpu/cpu.
source scripts/install_deepchem_conda.sh 3.7 cpu
If you want GPU support (we supports only CUDA 10.1):
source scripts/install_deepchem_conda.sh 3.7 gpu
If you are using the Windows and the PowerShell:
. .\scripts\install_deepchem_conda.ps1 3.7 cpu
(XXXX)in your command line.
conda init <YOUR_SHELL_NAME>to activate it, then:
conda activate deepchem pip install -e . pytest -m "not slow" deepchem # optional