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feat: create manorm container
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kelly-sovacool committed Dec 15, 2023
1 parent 5d49d1f commit 37da063
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96 changes: 96 additions & 0 deletions chipseq/ccbr_manorm/Dockerfile
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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/*
1 change: 1 addition & 0 deletions chipseq/ccbr_manorm/environment.txt
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manorm
4 changes: 4 additions & 0 deletions chipseq/ccbr_manorm/meta.yml
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dockerhub_namespace: nciccbr
image_name: ccbr_manorm
version: v1
container: "$(dockerhub_namespace)/$(image_name):$(version)"

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