Commit 8eb4c21e authored by nd-02110114's avatar nd-02110114
Browse files

🐳 fix dockerfile

parent 4419b3b6

README.md

+14 −10
Original line number Original line Diff line number Diff line
@@ -13,12 +13,12 @@ materials science, quantum chemistry, and biology. 




* [Requirements](#requirements)

* [Requirements](#requirements)

* [Installation](#installation)

* [Installation](#installation)

    * [Install latest package with conda](#install-via-conda-(Recommendation))

    * [Install latest package with conda](#install-via-conda-recommendation)

    * [Install latest package with pip (WIP)](#install-via-pip-(WIP))

    * [Install latest package with pip (WIP)](#install-via-pip-wip)

    * [Install from source](#install-from-source)

    * [Install from source](#install-from-source)

      * [OS except Windows](#os-except-windows)

      * [OS except Windows](#os-except-windows)

      * [Windows](#windows-(especially-powershell))

      * [Windows](#windows-especially-powershell)

    * [Install using a Docker with GPU (WIP)](#install-using-a-Docker-with-GPU-(WIP))

    * [Install using a Docker with GPU (WIP)](#install-using-a-docker-with-gpu-wip)

* [FAQ and Troubleshooting](#faq-and-troubleshooting)

* [FAQ and Troubleshooting](#faq-and-troubleshooting)

* [Getting Started](#getting-started)

* [Getting Started](#getting-started)

* [Contributing to DeepChem](/CONTRIBUTING.md)

* [Contributing to DeepChem](/CONTRIBUTING.md)
@@ -72,7 +72,7 @@ pip install joblib pandas pillow scikit-learn tensorflow deepchem 
```

```





### Install from 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**.  

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))

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.

First, please clone the deepchem repository from GitHub.
@@ -84,7 +84,7 @@ cd deepchem 




Then, follow each instruction on your OS.

Then, follow each instruction on your OS.





#### OS except Windows

### OS except Windows





If you want GPU support:

If you want GPU support:

```

```
@@ -108,15 +108,18 @@ nosetests -a '!slow' -v deepchem --nologcapture # Run tests 




Check [this link](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) for more information about the installation of conda environments.

Check [this link](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) for more information about the installation of conda environments.





#### Windows (especially powershell)

### Windows (especially powershell)





Currently you have to install from source in windows.

Currently you have to install from source in windows.





If you want gpu support, use the following command in powershell:

If you want gpu support, use the following command in powershell:



```ps1

```ps1

.\scripts\install_deepchem_conda.ps1 -gpu 1 deepchem

.\scripts\install_deepchem_conda.ps1 -gpu 1 deepchem

```

```

Or you can use the following command to install deepchem without gpu support.



Or use the following command to install deepchem without gpu support:



```ps1

```ps1

.\scripts\install_deepchem_conda.ps1 -gpu 0 deepchem

.\scripts\install_deepchem_conda.ps1 -gpu 0 deepchem

```

```
@@ -124,6 +127,7 @@ Or you can use the following command to install deepchem without gpu support. 
Before activating deepchem environment, make sure conda-powershell has been initialized.  

Before activating deepchem environment, make sure conda-powershell has been initialized.  

Check if there is a `(base)` before `PS` in powershell.  

Check if there is a `(base)` before `PS` in powershell.  

If not, use `conda init powershell` to activate it, then:

If not, use `conda init powershell` to activate it, then:



```

```

conda activate deepchem

conda activate deepchem

python setup.py install

python setup.py install
@@ -132,11 +136,11 @@ nosetests -a '!slow' -v deepchem --nologcapture 




### Install using a Docker with GPU (WIP)

### Install using a Docker with GPU (WIP)





#### Build the image from Dockerfile (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!

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)

### Use the official deepchem image (WIP)





This instruction is under development.

This instruction is under development.

docker/latest/Dockerfile

+7 −2
Original line number Original line Diff line number Diff line
@@ -9,7 +9,8 @@ RUN apt-get update && \ 
RUN MINICONDA="Miniconda3-latest-Linux-x86_64.sh" && \

RUN MINICONDA="Miniconda3-latest-Linux-x86_64.sh" && \

    wget --quiet https://repo.continuum.io/miniconda/$MINICONDA && \

    wget --quiet https://repo.continuum.io/miniconda/$MINICONDA && \

    bash $MINICONDA -b -p /miniconda && \

    bash $MINICONDA -b -p /miniconda && \

    rm -f $MINICONDA

    rm -f $MINICONDA && \

    echo ". /miniconda/etc/profile.d/conda.sh" >> ~/.bashrc

ENV PATH /miniconda/bin:$PATH

ENV PATH /miniconda/bin:$PATH





# install latest version deepchem

# install latest version deepchem
@@ -18,4 +19,8 @@ RUN conda update -n base conda && \ 
    . /miniconda/etc/profile.d/conda.sh && \

    . /miniconda/etc/profile.d/conda.sh && \

    conda init bash && \

    conda init bash && \

    conda activate deepchem && \

    conda activate deepchem && \

    conda install -c deepchem -c rdkit -c conda-forge -c omnia deepchem-gpu
 
    conda install -c deepchem -c rdkit -c conda-forge -c omnia deepchem-gpu==2.3.0 && \

    conda clean -afy



RUN echo "conda activate deepchem" >> ~/.bashrc

WORKDIR /root/mydir

docker/master/Dockerfile

+8 −2
Original line number Original line Diff line number Diff line
@@ -9,7 +9,8 @@ RUN apt-get update && \ 
RUN MINICONDA="Miniconda3-latest-Linux-x86_64.sh" && \

RUN MINICONDA="Miniconda3-latest-Linux-x86_64.sh" && \

    wget --quiet https://repo.continuum.io/miniconda/$MINICONDA && \

    wget --quiet https://repo.continuum.io/miniconda/$MINICONDA && \

    bash $MINICONDA -b -p /miniconda && \

    bash $MINICONDA -b -p /miniconda && \

    rm -f $MINICONDA

    rm -f $MINICONDA && \

    echo ". /miniconda/etc/profile.d/conda.sh" >> ~/.bashrc

ENV PATH /miniconda/bin:$PATH

ENV PATH /miniconda/bin:$PATH





# install deepchem with master branch

# install deepchem with master branch
@@ -19,4 +20,9 @@ RUN conda update -n base conda && \ 
    . /miniconda/etc/profile.d/conda.sh && \

    . /miniconda/etc/profile.d/conda.sh && \

    conda init bash && \

    conda init bash && \

    gpu=1 bash scripts/install_deepchem_conda.sh deepchem && \

    gpu=1 bash scripts/install_deepchem_conda.sh deepchem && \

    conda activate deepchem && python setup.py install
 
    conda activate deepchem && \

 No newline at end of file
 
    python setup.py install && \

    conda clean -afy



RUN echo "conda activate deepchem" >> ~/.bashrc

WORKDIR /root/mydir

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