From 5b7a01a299ac0a10c41844073bec5b6f39a16640 Mon Sep 17 00:00:00 2001 From: Joseph Salmingo Date: Tue, 12 Nov 2024 09:48:17 -0800 Subject: [PATCH] move Dockerfile --- docker/Dockerfile | 51 ----------------------------------------------- 1 file changed, 51 deletions(-) delete mode 100644 docker/Dockerfile diff --git a/docker/Dockerfile b/docker/Dockerfile deleted file mode 100644 index 0bd7e55..0000000 --- a/docker/Dockerfile +++ /dev/null @@ -1,51 +0,0 @@ -ARG MINIFORGE_VERSION=22.9.0-2 -ARG UBUNTU_VERSION=20.04 - -FROM condaforge/mambaforge:${MINIFORGE_VERSION} AS builder - -# Use conda to install tools and dependencies into /usr/local -ARG PYTHON_VERSION=3.10 -ARG VCFTOOLS_VERSION=0.1.16 -RUN mamba create -qy -p /usr/local \ - -c bioconda \ - -c conda-forge \ - python==${PYTHON_VERSION} \ - vcftools==${VCFTOOLS_VERSION} \ - perl-vcftools-vcf==${VCFTOOLS_VERSION} \ - tabix \ - pip - -# Deploy the target tools into a base image -FROM ubuntu:${UBUNTU_VERSION} AS final -COPY --from=builder /usr/local /usr/local - -RUN apt-get update && apt-get install -y --no-install-recommends \ - libmagic1 && \ - rm -rf /var/lib/apt/lists/* && \ - rm -rf /tmp/downloaded_packages/ /tmp/*.rds - -# create directory for python script -RUN mkdir -p /tool/validate/ - -# install all requirements, including validate module -# COPY requirements.txt /tool -COPY setup.py /tool -COPY setup.cfg /tool -COPY pyproject.toml /tool -COPY /pipeval /tool/pipeval -WORKDIR /tool -RUN pip install build && \ - pip install . - -# add tool folder to path -ENV PYTHONPATH "${PYTHONPATH}:/tool/" - -# Add a new user/group called bldocker -RUN groupadd -g 500001 bldocker && \ - useradd -r -u 500001 -g bldocker bldocker - -# Change the default user to bldocker from root -USER bldocker - -LABEL maintainer="Yash Patel " \ - org.opencontainers.image.source=https://github.com/uclahs-cds/package-PipeVal