Merge pull request #29 from CCBR/diffbind

feat: create container for diffbind

chipseq/ccbr_diffbind/Dockerfile

@@ -0,0 +1,97 @@
+FROM ubuntu:20.04
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+RUN mkdir -p /opt2 && mkdir -p /data2
+ENV TZ=America/New_York
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
+RUN apt update && apt-get -y upgrade
+# Set the locale
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+		locales build-essential cmake cpanminus && \
+	localedef -i en_US -f UTF-8 en_US.UTF-8 && \
+	cpanm FindBin Term::ReadLine
+
+# install basic dependencies with apt-get
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+    build-essential \
+	figlet \
+	g++ \
+	gcc \
+	gfortran \
+	git \
+	libatlas-base-dev \
+	libblas-dev \
+	libboost-dev \
+	libbz2-dev \
+	libcurl4-openssl-dev \
+	libexpat1-dev \
+	libfreetype6-dev \
+	libgd-dev \
+	libgd-perl \
+	libglib2.0-dev \
+    libgpgme11-dev \
+	libgs-dev \
+	libgsl-dev \
+	libgsl0-dev \
+	libhtml-template-compiled-perl \
+	libicu-dev \
+	libjudy-dev \
+	liblapack-dev \
+	liblzma-dev \
+	libmysqlclient-dev \
+	libncurses-dev \
+	libopenmpi-dev \
+	libpng-dev \
+	librtmp-dev \
+    libseccomp-dev \
+	libssl-dev \
+	libtool \
+	libxml-libxml-debugging-perl \
+	libxml-opml-simplegen-perl \
+	libxml2-dev \
+	libxslt-dev \
+	make \
+	manpages-dev \
+	openjdk-17-jre-headless \
+	parallel \
+	pigz \
+    pkg-config \
+	python3-pip \
+    python3-dev \
+	rsync \
+    squashfs-tools \
+	unzip \
+    uuid-dev \
+	wget \
+	zlib1g \
+	zlib1g-dev \
+	zlibc
+
+# Install conda and give write permissions to conda folder
+RUN echo 'export PATH=/opt2/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
+    wget --quiet "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O ~/miniforge3.sh && \
+    /bin/bash ~/miniforge3.sh -b -p /opt2/conda && \
+    rm ~/miniforge3.sh && chmod 777 -R /opt2/conda/
+ENV PATH="/opt2/conda/bin:$PATH"
+
+# install R packages from conda
+COPY environment.txt /data2/
+RUN mamba install -c bioconda -c conda-forge --file /data2/environment.txt
+ENV R_LIBS_USER=/opt2/conda/lib/R/library/
+
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+
+# cleanup
+WORKDIR /data2
+RUN apt-get clean && apt-get purge \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

chipseq/ccbr_diffbind/environment.txt

@@ -0,0 +1,5 @@
+bioconductor-diffbind
+r-base=4.3.2
+r-DT
+r-knitr
+r-rmarkdown

chipseq/ccbr_diffbind/meta.yml

@@ -0,0 +1,4 @@
+dockerhub_namespace: nciccbr
+image_name: ccbr_diffbind
+version: v1
+container: "$(dockerhub_namespace)/$(image_name):$(version)"