From 0acba4e3ffd606ba11e82697cb35245fde130c2a Mon Sep 17 00:00:00 2001
From: buehlere <buehlere@mskcc.org>
Date: Fri, 24 May 2024 17:21:22 -0400
Subject: [PATCH] Update Dockerfile

---
 Dockerfile | 79 +++++++++++++++++++++++++++++++++---------------------
 1 file changed, 49 insertions(+), 30 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 1fcd7b4..119a221 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,53 +1,72 @@
-################## Base Image ##########
-ARG PYTHON_VERSION="3.8"
-FROM --platform=linux/amd64 python:${PYTHON_VERSION}-slim
+################## BASE IMAGE ######################
+
+FROM ubuntu:latest
+
+################## ARGUMENTS########################
 
-################## ARGUMENTS/Environments ##########
 ARG BUILD_DATE
 ARG BUILD_VERSION
 ARG LICENSE="Apache-2.0"
-ARG GENOTYPE_VARIANTS_VERSION
-ARG GBCMS_VERSION="1.2.5"
+ARG GBCMS_VERSION=1.2.5
 ARG VCS_REF
-
 ################## METADATA ########################
+
 LABEL org.opencontainers.image.vendor="MSKCC"
-LABEL org.opencontainers.image.authors="Eric Buehler (buehlere@mskcc.org)"
+LABEL org.opencontainers.image.authors="Ronak Shah (shahr2@mskcc.org)"
 
 LABEL org.opencontainers.image.created=${BUILD_DATE} \
-    org.opencontainers.image.version=${BUILD_VERSION} \
-    org.opencontainers.image.licenses=${LICENSE} \
-    org.opencontainers.image.version.pvs=${GENOTYPE_VARIANTS_VERSION} \
-    org.opencontainers.image.vcs-url="https://github.com/msk-access/genotype_variants.git" \
-    org.opencontainers.image.vcs-ref=${VCS_REF}
+	org.opencontainers.image.version=${BUILD_VERSION} \
+	org.opencontainers.image.revision=${VCS_REF} \
+	org.opencontainers.image.licenses=${LICENSE} \
+	org.opencontainers.image.version.gbcms=${GBCMS_VERSION} \
+	org.opencontainers.image.source="https://github.com/msk-access/GetBaseCountsMultiSample/releases/"
 
-LABEL org.opencontainers.image.description="This container uses python3.8 as the base image to build \
-    genotype_variants ${GENOTYPE_VARIANTS_VERSION}"
+LABEL org.opencontainers.image.description="This container uses Ubuntu 16.04 as the base image to build GetBaseCountsMultiSample version ${GBCMS_VERSION}"
 
-ADD . /opt/genotype_variants
 ################## INSTALL ##########################
 
-# get build tools and install genotype variants
+WORKDIR /usr/src
 
-RUN apt-get update && apt-get install --no-install-recommends -y build-essential ca-certificates openssl gcc g++ make zlib1g-dev cmake libjsoncpp-dev curl unzip \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/*
+ADD . ./genotype_variants
 
-RUN cd /opt/ && \
-    curl -L -O "https://github.com/msk-access/GetBaseCountsMultiSample/archive/refs/tags/v${GBCMS_VERSION}.tar.gz" && \
-    tar xzvf v${GBCMS_VERSION}.tar.gz && \
-    cd /opt/GetBaseCountsMultiSample-${GBCMS_VERSION}/bamtools-master && \
-        rm -r build/ && \
+# Install Python Version
+RUN apt-get update && \
+    apt-get install -y software-properties-common && \
+    add-apt-repository ppa:deadsnakes/ppa && \
+    apt-get update && \
+    apt-get install -y python3.8 python3.8-dev python3.8-venv python3-pip && \
+    apt-get clean
+
+# Install GBCMS Dependencies
+RUN apt-get update && \
+	apt-get --no-install-recommends install -y \
+	wget ca-certificates openssl gcc g++ make zlib1g-dev cmake libjsoncpp-dev && \
+    apt-get clean autoclean && \
+	apt-get autoremove -y && \
+	rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Install GBCMS
+RUN wget --no-check-certificate "https://github.com/msk-access/GetBaseCountsMultiSample/archive/refs/tags/${GBCMS_VERSION}.tar.gz" && \
+	tar xzvf /usr/src/${GBCMS_VERSION}.tar.gz && \
+	cd /usr/src/GetBaseCountsMultiSample-${GBCMS_VERSION}/bamtools-master && \
+	rm -r build/ && \
         mkdir build && \
         cd build/ && \
         cmake -DCMAKE_CXX_FLAGS=-std=c++03 .. && \
         make && \
         make install && \
 	cp ../lib/libbamtools.so.2.3.0 /usr/lib/ && \
-    cd /opt/GetBaseCountsMultiSample-${GBCMS_VERSION} && \
+	cd /usr/src/GetBaseCountsMultiSample-${GBCMS_VERSION}/ && \
 	make && \
-    cp GetBaseCountsMultiSample /usr/local/bin/
+	cp GetBaseCountsMultiSample /usr/local/bin/
+
+# Create a virtual environment
+RUN python3.8 -m venv /opt/venv
+
+# Add the virtual environment's bin directory to the PATH
+ENV PATH="/opt/venv/bin:$PATH"
 
-RUN cd /opt/genotype_variants && \
-    pip install -r requirements_dev.txt && \
-    python setup.py install
+# Install Genotype_variants
+RUN cd /usr/src/genotype_variants && \
+    pip3 install -r requirements_dev.txt && \
+    python3 setup.py install