Update Dockerfile

Dockerfile

@@ -1,30 +1,74 @@
-FROM ubuntu:focal
+################## BASE IMAGE ######################
+FROM --platform=linux/amd64 ubuntu:22.04 as build
+# need to specify platform in case build is on arm64 system
 
-LABEL description="Image for homer software"
-LABEL maintainer="Matthew Galbraith <[email protected]>"
 
-ENV DEBIAN_FRONTEND=noninteractive
+################## 1st STAGE: SAMTOOLS INSTALLATION ######################
+ARG ENV_NAME="samtools"
+ARG VERSION="1.16.1"
 
-# Update apt-get
-RUN apt-get update \
-    ## Install HOMER dependencies
-    && apt-get install -y libnss-sss samtools r-base r-base-dev tabix wget libssl-dev libcurl4-openssl-dev libxml2-dev \
-    ## Remove packages in '/var/cache/' and 'var/lib'
-    ## to remove side-effects of apt-get update
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/*
+ENV DEBIAN_FRONTEND noninteractive
+ENV PACKAGES ca-certificates gcc mono-mcs libncurses5-dev libncursesw5-dev zlib1g zlib1g-dev bzip2 libbz2-dev liblzma-dev \
+    libhtscodecs2 build-essential wget libcurl4 libcurl4-gnutls-dev
+    # need libcurl4 and libcurl4-gnutls-dev for GCS access - see https://github.com/samtools/samtools/issues/862
 
-# Install required Bioconductor package(s) # SLOW and MAY NOT NEED THESE for tagdir and ucsc file creation
-RUN R -e 'install.packages("BiocManager")'
-RUN R -e 'BiocManager::install("edgeR")'
-RUN R -e 'BiocManager::install("DESeq2")'
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Get, configure, make, and install samtools 
+RUN wget https://github.com/samtools/samtools/releases/download/${VERSION}/samtools-${VERSION}.tar.bz2 && \
+    bzip2 -d samtools-${VERSION}.tar.bz2 && \
+    tar xvf samtools-${VERSION}.tar && \
+    cd samtools-${VERSION} && \
+    ./configure && \
+    make && \
+    make install
+
+
+################## 2ND STAGE: HOMER INSTALLATION ######################
+FROM --platform=linux/amd64 ubuntu:22.04
+
+################## METADATA ######################
+LABEL base_image="ubuntu:22.04"
+LABEL version="1.1.0"
+LABEL software="Homer"
+LABEL software.version.homer="4.11.1"
+LABEL software.version.samtools="1.9.0"
+LABEL about.summary="HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis."
+LABEL about.home="http://homer.ucsd.edu/homer/ "
+LABEL about.documentation="http://homer.ucsd.edu/homer/ "
+LABEL about.license_file=""
+LABEL about.license.homer="GPLv3"
+LABEL about.license.samtools="MIT/Expat"
+
+################## MAINTAINER ######################
+MAINTAINER Matthew Galbraith <[email protected]>
+
+ENV DEBIAN_FRONTEND noninteractive
+ENV PACKAGES libnss-sss r-base r-base-dev tabix wget ca-certificates libssl-dev libcurl4-openssl-dev libxml2-dev \
+    mono-mcs libncurses5-dev libncursesw5-dev zlib1g zlib1g-dev bzip2 libbz2-dev liblzma-dev libhtscodecs2
+# dependency samtools installed and copied from 1st stage to control version and save space
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+COPY --from=build /usr/local/bin/samtools/ /usr/local/bin
+
+# Install required Bioconductor package(s) # SLOW and MAY NOT NEED THESE for tagdir and ucsc file creation + may want to control R version? (looks like 3.6.3 is default)
+RUN R -e 'install.packages(c("BiocManager", "edgeR", "DESeq2"))'
 
 # Install and configure Homer
-RUN mkdir /opt/homer/ && cd /opt/homer && wget http://homer.ucsd.edu/homer/configureHomer.pl && /usr/bin/perl configureHomer.pl -install 
-# Genome information is too large
+# RUN mkdir /opt/homer/ && cd /opt/homer && wget http://homer.ucsd.edu/homer/configureHomer.pl && /usr/bin/perl configureHomer.pl -install # defaults to latest version
+RUN mkdir /opt/homer/ && cd /opt/homer && wget http://homer.ucsd.edu/homer/configureHomer.pl && /usr/bin/perl configureHomer.pl -install homer -version v4.11.1 # should install specific version
+
+# NOT USED: Genome & Annotation data is too large
 # RUN cd /opt/homer && /usr/bin/perl configureHomer.pl -install hg38 && /usr/bin/perl configureHomer.pl -install human-o
 
-# Annotation data is too large to include in this image, so it
+# Genome & Annotation data is too large to include in this image, so it
 # requires a directory to be mounted at /opt/homerdata/ containing
 #  - config.txt - homer configuration file with directories pointing to paths like "data/accession"
 #  - data  - folder containing homer annotation data files