DeepChem has a number of "soft" requirements. These are packages which are needed for various submodules of DeepChem but not for the package as a whole.
conda install-c deepchem -c rdkit -c conda-forge -c omnia deepchem=2.3.0
conda install-c deepchem -c rdkit -c conda-forge -c omnia deepchem
```
If you want GPU support:
```bash
conda install-c deepchem -c rdkit -c conda-forge -c omnia deepchem-gpu=2.3.0
conda install-c deepchem -c rdkit -c conda-forge -c omnia deepchem-gpu
```
**Note:** The above commands install the latest stable version of `deepchem` and _do not install from source_. If you need to install from source make sure you follow the steps [here](#using-a-conda-environment).
### Install via pip (WIP)
### Using a Docker Image
Using a docker image requires an NVIDIA GPU. If you do not have a GPU please follow the directions for [using a conda environment](#installing-from-source-in-a-conda-environment)
In order to get GPU support you will have to use the [nvidia-docker](https://github.com/NVIDIA/nvidia-docker) plugin.
``` bash
# This will the download the latest stable deepchem docker image into your images
docker pull deepchemio/deepchem
You are able to try to install deepchem via pip using the following command.
However, pip installation is under development, so this command may not work well.
# This will create a container out of our latest image with GPU support
nvidia-docker run -i-t deepchemio/deepchem
`deepchem>2.3`
# You are now in a docker container whose python has deepchem installed
You can install deepchem in a new conda environment using the conda commands in scripts/install_deepchem_conda.sh
Installing via this script will ensure that you are **installing from the source**.
### Install from source
You can install deepchem in a new conda environment using the conda commands in scripts/install_deepchem_conda.sh. Installing via this script will ensure that you are **installing from the source**.
The following script requires `conda>=4.4` because it uses the `conda activate` command. (Please see the detail from [here](https://github.com/conda/conda/blob/a4c4feae404b2b378e106bd25f62cc8be15c768f/CHANGELOG.md#440-2017-12-20))
First, please clone the deepchem repository from GitHub.
```bash
git clone https://github.com/deepchem/deepchem.git# Clone deepchem source code from GitHub
Note : `gpu=0 bash scripts/install_deepchem_conda.sh deepchem` will also install CPU supported `deepchem`.
Before activating deepchem environment, make sure conda has been initialized.
Check if there is a `(base)` in your command line.
If not, use `conda init bash (zsh, fish and so on)` to activate it, then:
```
source activate deepchem
conda activate deepchem
python setup.py install # Manual install
nosetests -a '!slow' -v deepchem --nologcapture # Run tests
```
This creates a new conda environment `deepchem` and installs in it the dependencies that
are needed. To access it, use the `conda activate deepchem` command (if your conda version >= 4.4) and use `source activate deepchem` command (if your conda version < 4.4).
Check [this link](https://conda.io/docs/using/envs.html) for more information about
the benefits and usage of conda environments. **Warning**: Segmentation faults can [still happen](https://github.com/deepchem/deepchem/pull/379#issuecomment-277013514)
via this installation procedure.
Check [this link](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) for more information about the installation of conda environments.
### Installing in Windows
#### Windows (especially powershell)
Currently you have to install from source in windows. The following scripts requires `conda>4.6`.
Currently you have to install from source in windows.
If you want gpu support, use the following command in powershell:
```ps1
@@ -125,14 +127,43 @@ Or you can use the following command to install deepchem without gpu support.
Before activating deepchem envrionment, make sure conda-powershell has been initialized.
Check if there is a `(base)` before `PS` in powershell. If not, use `conda init powershell`
to activate it, then:
Before activating deepchem environment, make sure conda-powershell has been initialized.
Check if there is a `(base)` before `PS` in powershell.
If not, use `conda init powershell`to activate it, then:
```
conda activate deepchem
python setup.py install
nosetests -a '!slow' -v deepchem --nologcapture
```
### Install using a Docker with GPU (WIP)
#### Build the image from Dockerfile (WIP)
We prepare for [sample Dockerfiles](https://github.com/deepchem/deepchem/tree/master/docker) to install deepchem from source codes and conda package manager. Please check them!
#### Use the official deepchem image (WIP)
This instruction is under development.
``` bash
# This will the download the latest stable deepchem docker image into your images
docker pull deepchemio/deepchem
# This will create a container out of our latest image with GPU support
nvidia-docker run -i-t deepchemio/deepchem
# You are now in a docker container whose python has deepchem installed
# For example you can run our tox21 benchmark
cd deepchem/examples
python benchmark.py -d tox21
# Or you can start playing with it in the command line
pip install jupyter
ipython
import deepchem as dc
```
## FAQ and Troubleshooting
1. DeepChem currently supports Python 3.5 through 3.7, and is supported on 64 bit Linux and Mac OSX. Note that DeepChem is not currently maintained for older versions of Python or with other operating systems.
