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Dockerfile
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FROM ubuntu:16.04
MAINTAINER Soo Lee ([email protected])
# 1. general updates & installing necessary Linux components
RUN apt-get update -y && apt-get install -y \
bzip2 \
gcc \
git \
less \
libncurses-dev \
make \
time \
unzip \
vim \
wget \
zlib1g-dev \
liblz4-tool
# installing python3.5 & pip
RUN apt-get update -y && apt-get install -y \
python3.5-dev \
python3-setuptools \
&& wget https://bootstrap.pypa.io/get-pip.py \
&& python3.5 get-pip.py
# installing java (for nozzle) - latest java version
RUN apt-get update -y && apt-get install -y default-jdk
# installing R & dependencies for pairsqc
# r-base, r-base-dev for R, libcurl4-openssl-dev, libssl-dev for devtools
RUN apt-get update -y && apt-get install -y \
libcurl4-openssl-dev \
libssl-dev \
r-base \
r-base-dev
RUN R -e 'install.packages("devtools", repos="http://cran.us.r-project.org")' \ # devtools
RUN R -e 'install.packages( "Nozzle.R1", type="source", repos="http://cran.us.r-project.org" )' \ # nozzle
RUN R -e 'library(devtools); install_url("https://github.com/SooLee/plotosaurus/archive/0.9.2.zip")' \ # plotosaurus
RUN R -e 'install.packages("stringr", repos="http://cran.us.r-project.org" )'
# installing conda
RUN wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh && bash Miniconda2-latest-Linux-x86_64.sh -p /miniconda2 -b
ENV PATH=/miniconda2/bin:$PATH
RUN conda update -y conda \
&& rm Miniconda2-latest-Linux-x86_64.sh
# installing gawk for juicer
RUN apt-get update -y && apt-get install -y gawk \
&& echo 'alias awk=gawk' >> ~/.bashrc
# download tools
WORKDIR /usr/local/bin
COPY downloads.sh .
RUN . downloads.sh
# set path
ENV PATH=/usr/local/bin/bwa/:$PATH
ENV PATH=/usr/local/bin/samtools/:$PATH
ENV PATH=/usr/local/bin/pairix/bin/:/usr/local/bin/pairix/util/:$PATH
ENV PATH=/usr/local/bin/pairix/util/bam2pairs/:$PATH
ENV PATH=/usr/local/bin/pairsqc/:$PATH
ENV PATH=/usr/local/bin/juicer/CPU/:/usr/local/bin/juicer/CPU/common:$PATH
ENV PATH=/usr/local/bin/hic2cool/:$PATH
ENV PATH=/usr/local/bin/mcool2hic/:$PATH
ENV PATH=/usr/local/bin/FastQC/:$PATH
# supporting UTF-8
ENV LC_ALL=C.UTF-8
ENV LANG=C.UTF-8
# wrapper
COPY scripts/ .
RUN chmod +x run*.sh
# default command
CMD ["run-list.sh"]