diff --git a/Dockerfile b/Dockerfile index 5365bb7..454415b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,13 +2,17 @@ FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.11.10 AS base-de SHELL ["/bin/bash", "-c"] +WORKDIR / + # Install system packages for HTSLib + SAMtools + curl and jq for workflows # OpenJDK is for running WOMtool/Cromwell -# Then, boostrap dependencies for setting up and running the Python application +# Then, install dependencies for running the Python server + Python workflow dependencies +COPY container.requirements.txt . RUN apt-get update -y && \ apt-get install -y samtools tabix bcftools curl jq openjdk-17-jre && \ rm -rf /var/lib/apt/lists/* && \ - pip install --no-cache-dir gunicorn==21.2.0 "pysam>=0.22.0,<0.23.0" + pip install --no-cache-dir -r /container.requirements.txt && \ + rm /container.requirements.txt WORKDIR / ENV CROMWELL_VERSION=86 @@ -22,8 +26,8 @@ FROM base-deps AS build-install RUN mkdir -p /wes/tmp && mkdir -p /data WORKDIR /wes -COPY pyproject.toml pyproject.toml -COPY poetry.lock poetry.lock +COPY pyproject.toml . +COPY poetry.lock . # Install production dependencies # Without --no-root, we get errors related to the code not being copied in yet. diff --git a/container.requirements.txt b/container.requirements.txt new file mode 100644 index 0000000..a986da5 --- /dev/null +++ b/container.requirements.txt @@ -0,0 +1,3 @@ +gunicorn==21.2.0 +pysam>=0.22.0,<0.23.0 +fasta-checksum-utils>=0.3.1,<0.4 diff --git a/dev.Dockerfile b/dev.Dockerfile index 2fb72c9..fd2d869 100644 --- a/dev.Dockerfile +++ b/dev.Dockerfile @@ -15,11 +15,13 @@ SHELL ["/bin/bash", "-c"] # Install system packages for HTSLib + SAMtools + curl and jq for workflows # OpenJDK is for running WOMtool/Cromwell -# Then, bootstrap dependencies for setting up and running the Python application +# Then, install dependencies for running the Python server + Python workflow dependencies +COPY container.requirements.txt . 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