diff --git a/chipseq/ccbr_manorm/Dockerfile b/chipseq/ccbr_manorm/Dockerfile new file mode 100644 index 0000000..e9eab99 --- /dev/null +++ b/chipseq/ccbr_manorm/Dockerfile @@ -0,0 +1,96 @@ +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:$PATH" + +# install packages from conda +COPY environment.txt /data2/ +RUN mamba install -c bioconda -c conda-forge --file /data2/environment.txt + +# Save Dockerfile in the docker +COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG} +RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG} + +# cleanup +WORKDIR /data2 +RUN apt-get clean && apt-get purge \ + && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* diff --git a/chipseq/ccbr_manorm/environment.txt b/chipseq/ccbr_manorm/environment.txt new file mode 100644 index 0000000..4fe92e6 --- /dev/null +++ b/chipseq/ccbr_manorm/environment.txt @@ -0,0 +1 @@ +manorm diff --git a/chipseq/ccbr_manorm/meta.yml b/chipseq/ccbr_manorm/meta.yml new file mode 100644 index 0000000..39f1232 --- /dev/null +++ b/chipseq/ccbr_manorm/meta.yml @@ -0,0 +1,4 @@ +dockerhub_namespace: nciccbr +image_name: ccbr_manorm +version: v1 +container: "$(dockerhub_namespace)/$(image_name):$(version)"