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Update Dockerfile and docs to use CMD instead of ENTRYPOINT #641

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merged 3 commits into from
Jul 23, 2024
Merged

Update Dockerfile and docs to use CMD instead of ENTRYPOINT #641

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ed9a0d0
Update docker to use CMD instead of ENTRYPOINT
jashapiro Jul 22, 2024
9972a4f
Update docs to suggest CMD instead of ENTRYPOINT
jashapiro Jul 22, 2024
3acd7c8
Missed entrypoint instruction
jashapiro Jul 22, 2024
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4 changes: 2 additions & 2 deletions analyses/cell-type-ewings/Dockerfile
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Expand Up @@ -65,5 +65,5 @@ RUN Rscript -e 'renv::restore()' && \
rm -rf /tmp/downloaded_packages && \
rm -rf /tmp/Rtmp*

# Set entrypoint to bash to activate the environment for any commands
ENTRYPOINT ["/bin/bash"]
# Set CMD to bash to activate the environment for any commands
CMD ["/bin/bash"]
1 change: 1 addition & 0 deletions analyses/doublet-detection/Dockerfile
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Expand Up @@ -62,4 +62,5 @@ RUN Rscript -e 'renv::restore()' \
# Activate conda environment on bash launch
RUN echo "conda activate ${ENV_NAME}" >> ~/.bashrc

# Set CMD to bash to activate the environment when launching
CMD ["/bin/bash"]
4 changes: 2 additions & 2 deletions analyses/hello-python/Dockerfile
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Expand Up @@ -25,5 +25,5 @@ RUN conda-lock install -n ${ENV_NAME} && \
# Activate conda environment on bash launch
RUN echo "conda activate ${ENV_NAME}" >> ~/.bashrc

# Set entrypoint to bash to activate the environment for any commands
ENTRYPOINT ["bash", "-l"]
# Set CMD to bash to activate the environment when launching
CMD ["/bin/bash"]
10 changes: 5 additions & 5 deletions docs/ensuring-repro/docker/docker-images.md
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Expand Up @@ -103,7 +103,7 @@ In the Dockerfile, you will want include the following steps:
- Install `conda-lock`.
- Copy the `conda-lock.yml` file from the host environment to the image.
- Use `conda-lock install` to create an environment from the `conda-lock.yml` file.
- Make sure the environment is activated when the container is launched by modifying the `.bashrc` file and setting the `ENTRYPOINT` to `bash -l -c`.
- Make sure the environment is activated when the container is launched by modifying the `.bashrc` file and setting the `CMD` to `/bin/bash`.

A simple `Dockerfile` for a conda-based analysis module that uses `conda-lock` for its environment might look like this:

Expand All @@ -127,8 +127,8 @@ RUN conda-lock install -n ${ENV_NAME} \
# Activate conda environment on bash launch
RUN echo "conda activate ${ENV_NAME}" >> ~/.bashrc

# Set entrypoint to bash to activate the environment for any commands
ENTRYPOINT ["bash", "-l", "-c"]
# Set CMD to bash to activate the environment when launching
CMD ["/bin/bash"]
```


Expand Down Expand Up @@ -188,8 +188,8 @@ RUN Rscript -e 'renv::restore()' \
# Activate conda environment on bash launch
RUN echo "conda activate ${ENV_NAME}" >> ~/.bashrc

# Set entrypoint to bash to activate the environment for any commands
ENTRYPOINT ["bash", "-l", "-c"]
# Set CMD to bash to activate the environment when launching
CMD ["/bin/bash"]
```

!!! tip
Expand Down