FROM centos:7

COPY CentOS-Base.repo /etc/yum.repos.d

RUN yum group install -y 'Development Tools' \

    && yum install -y epel-release \

    && yum install -y curl screen parallel \

         yum-utils \

        coreutils which binutils vim openssl-devel Xorg-devel mesa-libGL-devel \

        libxml-devel libxml2-devel \

        java-1.8.0-openjdk wget pigz gawk \

    && yum-builddep -y R

RUN mkdir -p /apps/archive

# install R

RUN wget --quiet -P /apps/archive 'https://mran.blob.core.windows.net/install/mro/3.5.3/rhel/microsoft-r-open-3.5.3.tar.gz'

RUN tar -C /apps/archive -zxf /apps/archive/microsoft-r-open-3.5.3.tar.gz

RUN bash /apps/archive/microsoft-r-open/install.sh -s -a -u

# install R packages

# COPY install-R-packages.R R-packages.txt /apps/archive/

COPY install-R-packages.R /apps/archive/

RUN cd /apps/archive; Rscript /apps/archive/install-R-packages.R

# install anaconda3

RUN wget --quiet -P /apps/archive 'https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh' \

    && bash /apps/archive/Anaconda3-2019.03-Linux-x86_64.sh -b -p /apps/anaconda3

# install anaconda2

RUN wget --quiet -P /apps/archive 'https://repo.anaconda.com/archive/Anaconda2-2019.03-Linux-x86_64.sh' \

    && bash /apps/archive/Anaconda2-2019.03-Linux-x86_64.sh -b -p /apps/anaconda2

# install pip packages

RUN /apps/anaconda3/bin/pip install skrebate \

    && /apps/anaconda3/bin/conda install -c conda-forge datrie \

    && /apps/anaconda3/bin/pip install mlxtend tqdm flask flask-AutoIndex jinja2 umap snakemake pyBigWig

# install conda packages

RUN /apps/anaconda3/bin/conda install -y numpy scipy scikit-learn 'openssl<1.1' \

    && /apps/anaconda3/bin/conda install -y pandas matplotlib seaborn h5py bokeh \

    && /apps/anaconda3/bin/conda install -c conda-forge jupyterhub \

    && /apps/anaconda3/bin/conda install -c bioconda -y bedtools samtools star subread bowtie2 \

    && /apps/anaconda3/bin/conda install -c bioconda -y rsem bamtools cutadapt picard gffread gffcompare \

    && /apps/anaconda3/bin/conda install -c bioconda -y ucsc-bedtogenepred ucsc-genepredtogtf ucsc-bedgraphtobigwig ucsc-bigwigtobedgraph \

    && /apps/anaconda3/bin/conda install -c bioconda -y htseq fastx_toolkit biopython \

    && /apps/anaconda3/bin/conda install -c bioconda -y multiqc fastqc

# Jupyter

RUN /apps/anaconda3/bi/conda install -y -c conda-forge jupyterhub \

    && /apps/anaconda3/bin/conda install notebook \

    && /usr/bin/R --slave -e "install.packages('IRkernel');IRkernel::installspec(user = FALSE);"

# UCSC kent tools

RUN rsync -aP rsync://hgdownload-sd.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ /apps/ucsc_tools/ \

    && rm -f /apps/ucsc_tools/FOOTER.txt \

    && chmod +x /apps/ucsc_tools/*

# cleanup 

RUN /apps/anaconda3/bin/conda clean -y --all \

    && yum clean all

# Download exSeek

RUN git clone https://github.com/ltbyshi/exSeek.git /apps/exSeek

ENV PATH=/apps/exseek/bin:/apps/ucsc_tools:/opt/microsoft/ropen/3.5.3/lib64/R/bin:/apps/anaconda3/bin:/apps/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin