This exact Dockerfile was working 2 weeks ago and I can't figure out why it's not workingnow. Nothing has changed in the script.
Here's the Dockerfile
# v2023.6.6
# =================================
# Miniconda3
# =================================
FROM continuumio/miniconda3
ARG ENV_NAME
SHELL ["/bin/bash","-l", "-c"]
WORKDIR /root/
# Data
RUN mkdir -p /volumes/input
RUN mkdir -p /volumes/output
RUN mkdir -p /volumes/database
# Retrieve VEBA repository
RUN mkdir -p veba/
COPY ./install/ veba/install/
COPY ./src/ veba/src/
COPY ./VERSION veba/VERSION
COPY ./LICENSE veba/LICENSE
# Install Miniconda
RUN /opt/conda/bin/conda init bash && \
/opt/conda/bin/conda config --add channels jolespin && \
/opt/conda/bin/conda config --add channels bioconda && \
/opt/conda/bin/conda config --add channels conda-forge && \
/opt/conda/bin/conda update conda -y && \
# /opt/conda/bin/conda install -c conda-forge mamba -y && \ # Mamba adds about 450 MB to image
# /opt/conda/bin/mamba init bash && \
/opt/conda/bin/conda clean -afy
# =================================
# Add conda bin to path
ENV PATH /opt/conda/bin:$PATH
# Create environment
RUN conda env create -n ${ENV_NAME} -f veba/install/environments/${ENV_NAME}.yml
# RUN mamba env create -n ${ENV_NAME} -f veba/install/environments/${ENV_NAME}.yml
# Add environment scripts to environment bin
RUN /bin/bash veba/install/update_environment_scripts.sh veba/
# # Add contents to path
# ENV PATH /opt/conda/envs/${ENV_NAME}/bin:$PATH
# Set up environment
RUN echo "conda activate ${ENV_NAME}" >> ~/.bashrc
# Set entrypoint to bash
ENTRYPOINT ["bash", "-l", "-c"]
Here's my environment.yml file
Last time I built this image, my dockerfile created exactly as expected. Now it's not even installing pandas. I tried launching a docker container and manually installing. No errors were thrown but it didn't install any of the dependencies.
This is from within the Docker container in an interactive session:
(base) root@c3be34361e98:~# conda env create -n test_env -f veba/install/environments/VEBA-preprocess_env.yml
Collecting package metadata (repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.5.0
latest version: 23.7.2
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.7.2
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate test_env
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) root@c3be34361e98:~# conda activate test_env
(test_env) root@c3be34361e98:~# conda env list
# conda environments:
#
base /opt/conda
test_env * /opt/conda/envs/test_env
(test_env) root@c3be34361e98:~# conda list
# packages in environment at /opt/conda/envs/test_env:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
dependencies 7.7.0 pyhd8ed1ab_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.1.0 he5830b7_0 conda-forge
libgomp 13.1.0 he5830b7_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libsqlite 3.42.0 h2797004_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
ncurses 6.4 hcb278e6_0 conda-forge
openssl 3.1.1 hd590300_1 conda-forge
pip 23.2.1 pyhd8ed1ab_0 conda-forge
python 3.11.4 hab00c5b_0_cpython conda-forge
readline 8.2 h8228510_1 conda-forge
setuptools 68.0.0 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
wheel 0.41.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
My question:
Why is my conda not installing the dependencies within the Docker container?
The environment part works fine with the latest Micromamba image:
FROM mambaorg/micromamba:1.4.9
COPY --chown=$MAMBA_USER:$MAMBA_USER VEBA-preprocess_env.yml /tmp/env.yml
RUN micromamba install -yn base -f /tmp/env.yml && \
micromamba clean -qafy
Consider starting over from this, since it implements some better practices and vastly simplifies the boiler plate. Note rather than using a second environment, we simply just put everything in base, and with Micromamba, there isn't anything else in base but your environment specification. See the micromamba-docker documentation.