From 08f04d746f0c437ba87e5749efd9dab75b333e88 Mon Sep 17 00:00:00 2001 From: Kohulan Date: Mon, 30 Sep 2024 15:56:29 +0200 Subject: [PATCH] fix: open babel installation issues --- Dockerfile | 4 ++-- Dockerfile.lite | 8 ++------ 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/Dockerfile b/Dockerfile index e521153..947dc17 100644 --- a/Dockerfile +++ b/Dockerfile @@ -18,7 +18,7 @@ RUN mv surge /usr/bin RUN conda install -c conda-forge python=${PYTHON_VERSION} sqlite --force-reinstall #RUN conda install -c conda-forge rdkit==RDKIT_VERSION -RUN conda install -c conda-forge openbabel>=OPENBABEL_VERSION +#RUN conda install -c conda-forge openbabel RUN python3 -m pip install -U pip @@ -32,7 +32,7 @@ RUN pip3 install --upgrade setuptools pip RUN pip3 install --no-cache-dir -r /code/requirements.txt RUN python3 -m pip uninstall -y imantics RUN pip3 install imantics==0.1.12 -RUN pip3 install rdkit +RUN pip3 install rdkit openbabel-wheel RUN pip3 install --no-deps decimer-segmentation==1.1.3 RUN pip3 install --no-deps decimer==2.3.0 RUN pip3 install --no-deps STOUT-pypi==2.0.5 diff --git a/Dockerfile.lite b/Dockerfile.lite index 68af915..bfb667f 100644 --- a/Dockerfile.lite +++ b/Dockerfile.lite @@ -2,7 +2,6 @@ FROM continuumio/miniconda3:24.1.2-0 AS cheminf-python-ms ENV PYTHON_VERSION=3.11 ENV RDKIT_VERSION=2023.09.4 -ENV OPENBABEL_VERSION=v3.1.1 ENV INCLUDE_OCSR=false # Install runtime dependencies RUN apt-get update && \ @@ -17,22 +16,19 @@ RUN chmod +x surge RUN mv surge /usr/bin RUN conda install -c conda-forge python=${PYTHON_VERSION} sqlite --force-reinstall -#RUN conda install -c conda-forge rdkit==RDKIT_VERSION -RUN conda install -c conda-forge openbabel>=OPENBABEL_VERSION - RUN python3 -m pip install -U pip ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/ RUN export JAVA_HOME WORKDIR /code -COPY ./requirements.txt /code/requirements.txt +COPY ./requirements_lite.txt /code/requirements_lite.txt RUN pip3 install --upgrade setuptools pip RUN pip3 install --no-cache-dir -r /code/requirements_lite.txt RUN python3 -m pip uninstall -y imantics RUN pip3 install imantics==0.1.12 -RUN pip3 install rdkit +RUN pip3 install rdkit openbabel-wheel RUN pip3 install --no-deps STOUT-pypi==2.0.5 RUN python3 -m pip install uvicorn[standard]