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BacRNADock
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FROM ubuntu:xenial
RUN apt-get update --fix-missing -qq && apt-get install -y -q \
aufs-tools \
automake \
build-essential \
cmake \
curl \
g++ \
openjdk-8-jre \
openjdk-8-jdk \
locales \
libncurses5-dev \
libncursesw5-dev \
libcurl4-openssl-dev \
libbz2-dev \
libx11-dev \
pkg-config \
zlib1g-dev \
bzip2 \
r-base \
default-jre \
git-core \
bc \
unzip \
wget \
xutils-dev \
&& apt-get clean \
&& apt-get purge
RUN apt-get update --fix-missing -qq && apt-get install -y -q \
software-properties-common
RUN add-apt-repository ppa:deadsnakes/ppa
RUN apt-get update --fix-missing -qq && apt-get install -y -q \
python3.7 \
python3-pip
RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.7 1
RUN python --version
RUN python -m pip install --upgrade pip
RUN python -m pip install numpy
RUN python -m pip install scipy
RUN python -m pip install biopython
RUN python -m pip install git+https://github.com/katholt/srst2
# RUN python2.7 -m pip install RSeQC
RUN python -m pip install multiqc
RUN python -m pip install venn
RUN python -m pip install pandas
# install Picard Tools
RUN curl -fksSL https://github.com/broadinstitute/picard/releases/download/2.9.0/picard.jar > /usr/local/bin/picard.jar && \
chmod +x /usr/local/bin/picard.jar
## Install R packages for ggplot2
RUN R -e 'install.packages( c("reshape2","optparse", "BiocManager"), repos="http://cloud.r-project.org/");' && \
apt-get update && apt-get install r-cran-ggplot2 -y -q
RUN R -e 'BiocManager::install("dupRadar");'
################################################################################################
WORKDIR /
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ENV PATH /opt/conda/bin:$PATH
RUN apt-get update --fix-missing && apt-get install -y wget bzip2 ca-certificates \
libglib2.0-0 libxext6 libsm6 libxrender1 \
git mercurial subversion
RUN wget --quiet https://repo.anaconda.com/archive/Anaconda3-5.3.0-Linux-x86_64.sh -O ~/anaconda.sh && \
/bin/bash ~/anaconda.sh -b -p /opt/conda && \
rm ~/anaconda.sh && \
ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
echo "conda activate base" >> ~/.bashrc
RUN apt-get install -y curl grep sed dpkg && \
TINI_VERSION=`curl https://github.com/krallin/tini/releases/latest | grep -o "/v.*\"" | sed 's:^..\(.*\).$:\1:'` && \
curl -L "https://github.com/krallin/tini/releases/download/v${TINI_VERSION}/tini_${TINI_VERSION}.deb" > tini.deb && \
dpkg -i tini.deb && \
rm tini.deb && \
apt-get clean
RUN conda install -c hcc resistomeanalyzer
RUN conda install -c bioconda trimmomatic
RUN conda install -c bioconda fastqc
RUN conda install -c bioconda picard=2.18.27
RUN conda install -c conda-forge gsl
RUN conda install -c bioconda trim-galore
RUN conda install -c bioconda cutadapt
RUN conda install -c bioconda fastx_toolkit
RUN conda install -c bioconda gffread=0.9.12
RUN conda install -c bioconda deeptools=3.2.0
RUN conda install -c bioconda sra-tools
RUN conda install -c bioconda bioconductor-dupradar=1.12.1
RUN conda install -c bioconda samtools
RUN conda install -c bioconda star
RUN conda install -c bioconda bwa
RUN conda install -c bioconda salmon
RUN conda install -c bioconda stringtie
RUN conda install -c bioconda bowtie2
RUN conda install -c bioconda bedtools
RUN conda install -c bioconda sortmerna
# R related nonsense
#RUN conda install -c bioconda bioconductor-deseq2
RUN conda install -c bioconda conda-forge::r-data.table=1.12.0
RUN conda install -c bioconda conda-forge::r-gplots=3.0.1.1
RUN conda install -c bioconda conda-forge::r-markdown=0.9
RUN conda install -c bioconda rsem
RUN conda install -c bioconda bioconductor-rsubread
# Visualisation
RUN conda install -c bioconda circos
# Build this image
#docker build -t bacterial_transcriptomics -f BacRNADock .
# To build sing image
#docker run -v /var/run/docker.sock:/var/run/docker.sock -v /Volumes/External/BacRNADock:/output --privileged -t --rm singularityware/docker2singularity:v2.6 -m "/shared_fs /custom_mountpoint2" bacterial_transcriptomics:latest
# To SCP
# scp /Volumes/External/BacRNADock/<image> [email protected]:/cbio/users/jambler/images/