From 5df4c9544bb89b8925a05dca9d5079f69b896eff Mon Sep 17 00:00:00 2001
From: Joseph Salmingo <jsalmingo@mednet.ucla.edu>
Date: Tue, 12 Nov 2024 09:49:58 -0800
Subject: [PATCH] add Dockerfile to base dir

---
 Dockerfile | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..0bd7e55
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,51 @@
+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 <yashpatel@mednet.ucla.edu>" \
+        org.opencontainers.image.source=https://github.com/uclahs-cds/package-PipeVal