:whale: fix dockerfile (8eb4c21e) · Commits · 钟慕尧 / deepchem

README.md

+14 −10

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		@@ -13,12 +13,12 @@ materials science, quantum chemistry, and biology.

		* [Requirements](#requirements)
		* [Installation](#installation)
		* [Install latest package with conda](#install-via-conda-(Recommendation))
		* [Install latest package with pip (WIP)](#install-via-pip-(WIP))
		* [Install latest package with conda](#install-via-conda-recommendation)
		* [Install latest package with pip (WIP)](#install-via-pip-wip)
		* [Install from source](#install-from-source)
		* [OS except Windows](#os-except-windows)
		* [Windows](#windows-(especially-powershell))
		* [Install using a Docker with GPU (WIP)](#install-using-a-Docker-with-GPU-(WIP))
		* [Windows](#windows-especially-powershell)
		* [Install using a Docker with GPU (WIP)](#install-using-a-docker-with-gpu-wip)
		* [FAQ and Troubleshooting](#faq-and-troubleshooting)
		* [Getting Started](#getting-started)
		* [Contributing to DeepChem](/CONTRIBUTING.md)
		@@ -72,7 +72,7 @@ pip install joblib pandas pillow scikit-learn tensorflow deepchem
		```

		### 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))

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

		Then, follow each instruction on your OS.

		#### OS except Windows
		### OS except Windows

		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.

		#### Windows (especially powershell)
		### Windows (especially powershell)

		Currently you have to install from source in windows.

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

		```ps1
		.\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
		.\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.
		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
		@@ -132,11 +136,11 @@ nosetests -a '!slow' -v deepchem --nologcapture

		### 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!

		#### Use the official deepchem image (WIP)
		### Use the official deepchem image (WIP)

		This instruction is under development.

docker/latest/Dockerfile

+7 −2

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		@@ -9,7 +9,8 @@ RUN apt-get update && \
		RUN MINICONDA="Miniconda3-latest-Linux-x86_64.sh" && \
		wget --quiet https://repo.continuum.io/miniconda/$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

		# install latest version deepchem
		@@ -18,4 +19,8 @@ RUN conda update -n base conda && \
		. /miniconda/etc/profile.d/conda.sh && \
		conda init bash && \
		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	Diff line number	Diff line
		@@ -9,7 +9,8 @@ RUN apt-get update && \
		RUN MINICONDA="Miniconda3-latest-Linux-x86_64.sh" && \
		wget --quiet https://repo.continuum.io/miniconda/$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

		# install deepchem with master branch
		@@ -19,4 +20,9 @@ RUN conda update -n base conda && \
		. /miniconda/etc/profile.d/conda.sh && \
		conda init bash && \
		gpu=1 bash scripts/install_deepchem_conda.sh deepchem && \
		conda activate deepchem && python setup.py install
		No newline at end of file
		conda activate deepchem && \
		python setup.py install && \
		conda clean -afy

		RUN echo "conda activate deepchem" >> ~/.bashrc
		WORKDIR /root/mydir

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