-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
updated base for conda env build and management rather than poetry
- Loading branch information
1 parent
f631bb7
commit 1b60010
Showing
4 changed files
with
170 additions
and
72 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,121 @@ | ||
| # FROM ghcr.io/biosimulators/biosimulators:latest THE STABLE VERSION OF BIOSIMULATOR PROCESSES IMAGE IS 0.0.4 | ||
| # FROM ghcr.io/vivarium-collective/biosimulator-processes:0.0.4 | ||
|
|
||
| FROM ubuntu:22.04 | ||
|
|
||
| LABEL authors="alexanderpatrie" | ||
|
|
||
| ENV DEBIAN_FRONTEND=noninteractive | ||
| ENV MONGO_URI="mongodb://mongodb/?retryWrites=true&w=majority&appName=bio-check" | ||
|
|
||
| # handle app creds from google | ||
| RUN mkdir /.google | ||
| COPY ./assets/.biosimulations.json /.google/.bio-check.json | ||
| # COPY ./.bio-check.json /.google/.bio-check.json | ||
|
|
||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| python3.10 \ | ||
| ca-certificates \ | ||
| libhdf5-dev \ | ||
| libhdf5-serial-dev \ | ||
| python3-pip \ | ||
| python3-dev \ | ||
| build-essential \ | ||
| libncurses5 \ | ||
| libxml2 \ | ||
| cmake \ | ||
| make \ | ||
| libx11-dev \ | ||
| libc6-dev \ | ||
| libx11-6 \ | ||
| libgl1-mesa-dev \ | ||
| libc6 \ | ||
| gcc \ | ||
| libatlas-base-dev \ | ||
| swig \ | ||
| pkg-config \ | ||
| curl \ | ||
| tar \ | ||
| libgl1-mesa-glx \ | ||
| libice6 \ | ||
| libpython3.10 \ | ||
| libsm6 \ | ||
| wget | ||
|
|
||
| # hdf5/amici env deps | ||
| RUN apt-get update && apt-get install -y libatlas-base-dev libhdf5-serial-dev swig libboost-all-dev gnupg | ||
|
|
||
| # handle main content | ||
| WORKDIR /app | ||
|
|
||
| RUN mkdir /app/data | ||
|
|
||
| # copy assets | ||
| COPY ./assets/requirements.base.txt ./assets/scripts/remove_deps.sh ./assets/scripts/update_deps.sh ./assets/dropped.txt ./assets/scripts/install_deps.sh /app/assets/ | ||
| COPY pyproject.toml poetry.lock /app/ | ||
|
|
||
| # Configure PySCeS from assets | ||
| COPY ./assets/.pys_usercfg.ini /Pysces/.pys_usercfg.ini | ||
| COPY ./assets/.pys_usercfg.ini /root/Pysces/.pys_usercfg.ini | ||
| RUN mkdir -p /Pysces \ | ||
| && mkdir -p /Pysces/psc \ | ||
| && mkdir -p /root/Pysces \ | ||
| && mkdir -p /root/Pysces/psc \ | ||
| && chmod ugo+rw -R /Pysces | ||
|
|
||
| # copy example files TODO: optimize this. | ||
| COPY ./model-examples/sbml-core/Elowitz-Nature-2000-Repressilator.omex /app/data/Elowitz-Nature-2000-Repressilator.omex | ||
| COPY ./model-examples/sbml-core/Elowitz-Nature-2000-Repressilator /app/data/Elowitz-Nature-2000-Repressilator | ||
|
|
||
| # create readme for poetry | ||
| RUN echo "BioCompose Server" > /app/README.md | ||
|
|
||
| # install poetry and deps | ||
| RUN python3.10 -m pip install --upgrade pip \ | ||
| && python3.10 -m pip install poetry \ | ||
| && poetry config virtualenvs.in-project true \ | ||
| && poetry env use 3.10 \ | ||
| && poetry install --without=api,worker,pysces,masspy | ||
|
|
||
|
|
||
| # install smoldyn | ||
| # RUN . /app/.venv/bin/activate \ | ||
| # && wget https://www.smoldyn.org/smoldyn-2.73.tgz \ | ||
| # && tar -xzf smoldyn-2.73.tgz \ | ||
| # && cd smoldyn-2.73 \ | ||
| # && cd build \ | ||
| # && cmake .. -DENABLE_PYTHON=ON -DPYTHON_EXECUTABLE=$(which python3.10) \ | ||
| # && make \ | ||
| # && make install | ||
| # && rm -rf /var/lib/apt/lists/* \ | ||
| # && apt-get clean \ | ||
| # && apt-get autoclean | ||
|
|
||
| # RUN . /app/.venv/bin/activate \ | ||
| # && curl -O https://download.opensuse.org/repositories/home:/dilawar/xUbuntu_22.04/amd64/smoldyn_2.64.4-1+2.1_amd64.deb \ | ||
| # && dpkg -i smoldyn_2.64.4-1+2.1_amd64.deb | ||
|
|
||
| # RUN . /app/.venv/bin/activate \ | ||
| # && echo 'deb http://download.opensuse.org/repositories/home:/dilawar/xUbuntu_22.04/ /' | tee /etc/apt/sources.list.d/home:dilawar.list \ | ||
| # && curl -fsSL https://download.opensuse.org/repositories/home:dilawar/xUbuntu_22.04/Release.key | gpg --dearmor | tee /etc/apt/trusted.gpg.d/home_dilawar.gpg > /dev/null \ | ||
| # && apt update \ | ||
| # && apt install smoldyn | ||
|
|
||
| # fix python version constraint, lock env, and check compatible | ||
| # RUN sed -i 's/python = ">=3.10"/python = "^3.10"/' /app/pyproject.toml \ | ||
| # && poetry lock \ | ||
| # && poetry check | ||
|
|
||
| # TODO: fix this eventually, but for now (10/2024) biosimulators-processes is not used | ||
| # RUN rm -r biosimulator_processes | ||
|
|
||
| # remove existing cobra installation TODO: clean this up | ||
| # RUN poetry remove cobra && poetry remove zarr | ||
|
|
||
| # install project deps (shared) | ||
| # RUN chmod +x /app/assets/install_deps.sh \ | ||
| # && /app/assets/install_deps.sh /app/assets/requirements.base.txt | ||
|
|
||
|
|
||
| # TODO: create shared tooling module which is a set of the sum of api and worker data_model.py & shared.py | ||
| # COPY ./assets/shared.py /app/shared.py |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| name: base | ||
| channels: | ||
| - defaults | ||
| - conda-forge | ||
| dependencies: | ||
| - python=3.8 | ||
| - numpy | ||
| - flask | ||
| - pip | ||
| - pip: | ||
| - requests | ||
| - some-other-pip-package |