Commit 728cb16f authored by jspiegel's avatar jspiegel

Fix Docker dependencies, expand README

parent 16938776
......@@ -34,6 +34,26 @@ We strongly recommend running AutoGrow4 via Docker using
`/autogrow4/docker/autogrow_in_docker.py`. See the tutorial at
`/autogrow4/tutorial/TUTORIAL.md` for more details.
## Dependencies
AutoGrow4 version 4.0.1 has been tested to run using the following dependencies:
```python
>>> rdkit.__version__
'2019.03.4'
>>> numpy.__version__
'1.17.2'
>>> scipy.__version__
'1.4.1'
>>> matplotlib.__version__
'3.1.1'
```
If you are unable to run AutoGrow4, please try running AutoGrow4 in an environment
using these releases these dependencies, or the Docker version of AutoGrow4 which
automatically installs dependencies verified to work with AutoGrow4. If you discover
AutoGrow4 is no longer compatible with current library releases, please contact us
and we will attempt to correct the code.
## Developer Note
Dimorphite is Version 1.2.3 with the citation print statements silenced.
......
......@@ -19,15 +19,16 @@ RUN chmod -R a+rwx Miniconda3-latest-Linux-x86_64.sh
RUN ./Miniconda3-latest-Linux-x86_64.sh -b
RUN rm ./Miniconda3-latest-Linux-x86_64.sh
RUN echo "alias python=/root/miniconda3/bin/python" >> /root/.bashrc
RUN echo "alias conda=/root/miniconda3/bin/conda" >> /root/.bashrc
RUN echo "alias pip=/root/miniconda3/bin/pip" >> /root/.bashrc
# Get python dependencies
RUN /root/miniconda3/bin/conda install -y -c conda-forge rdkit rdkit="2019.03.4"
RUN /root/miniconda3/bin/conda install -y numpy
RUN /root/miniconda3/bin/conda install -y scipy
RUN /root/miniconda3/bin/pip install matplotlib
RUN /root/miniconda3/bin/pip install func-timeout
RUN conda install -y -c conda-forge rdkit rdkit=2020.03.1
RUN conda install -y numpy numpy=1.18.1
RUN conda install -y scipy scipy=1.4.1
RUN pip install matplotlib matplotlib=3.2.1
RUN pip install func-timeout func_timeout=4.3.5
# Install mgltools
RUN wget http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_x86_64Linux2_1.5.6.tar.gz
......
......@@ -84,3 +84,21 @@ To run AutoGrow4 in a docker, please use the `autogrow_in_docker.py` script:
image's ENTRYPOINT runs this script. It is automatically switched by
`autogrow_in_docker.py`
- `Dockerfile`: Docker instructions re. how to build the image.
### Developer Notes
- AutoGrow4's Docker has been tested and fixed to install the following dependencies:
```python
>>> rdkit.__version__
'2019.03.4'
>>> numpy.__version__
'1.17.2'
>>> scipy.__version__
'1.4.1'
>>> matplotlib.__version__
'3.1.1'
```
- Please test and update `$PATH/docker/Dockerfile` these as new versions of AutoGrow4 and
these dependences are released.
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