VarDock

FROM ubuntu:xenial

RUN apt-get update --fix-missing -qq && apt-get install -y -q \
    curl \
    locales \
    libncurses5-dev  \
    libncursesw5-dev \
    build-essential \
    pkg-config \
    zlib1g-dev \
    bzip2 \
    r-base \
    default-jre \
    git-core \
    bc \
    python3 \
    wget \
    python-pip \
    && apt-get clean \
    && apt-get purge


RUN pip install --upgrade pip
RUN pip install numpy

# 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 SAMtools
RUN curl -fksSL https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 | tar xj && \
    cd samtools-1.3.1 && \
    make all all-htslib && make install install-htslib

# install VCFtools
RUN curl -fksSL https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz | tar xz && \
    cd vcftools-0.1.14 && \
    ./configure; make; make install

# install STAR
RUN curl -fksSL https://github.com/alexdobin/STAR/archive/2.5.2b.tar.gz | tar xz && \
    cp STAR-2.5.2b/bin/Linux_x86_64/* /usr/local/bin

# install bwe-mem
RUN git clone https://github.com/lh3/bwa.git && cd bwa; make; cp bwa /usr/local/bin

# Install freebayes
RUN git clone --recursive https://github.com/ekg/freebayes && cd freebayes && make; make install

# Install BCFTools
RUN git clone git://github.com/samtools/htslib.git; cd htslib && make && make install
RUN git clone git://github.com/samtools/bcftools.git; cd bcftools; autoheader && autoconf && ./configure --enable-libgsl --enable-perl-filters; make

# Install SnpEff
RUN curl -L http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip > snpEff_latest_core.zip && unzip snpEff_latest_core.zip

# Install vcf2fasta
RUN git clone https://github.com/jambler24/vcf2fasta.git && cd vcf2fasta && chmod a+x process_samples.py && chmod a+x vcf2fasta.py

# Install convbioseq
RUN easy_install biopython
RUN easy_install bioscripts.convert

# Install RAxML
RUN git clone https://github.com/stamatak/standard-RAxML.git && cd standard-RAxML* && \
    make -f Makefile.AVX.gcc && \
    rm *.o && \
    make -f Makefile.AVX.PTHREADS.gcc

# RUN pip install VCF-kit
# RUN vk setup

## Install R packages for ggplot2
RUN R -e 'install.packages( c("reshape2","optparse"), repos="http://cloud.r-project.org/");' && \
    apt-get update && apt-get install r-cran-ggplot2 -y -q

# Install SRA toolkit
RUN wget "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.2/sratoolkit.2.9.2-ubuntu64.tar.gz" && \
   tar -xzf sratoolkit.2.9.2-ubuntu64.tar.gz
ENV PATH "$PATH:/sratoolkit.2.9.2-ubuntu64/bin/:/vcf2fasta/"

# Install trimmomatic

RUN curl -L http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip > Trimmomatic-0.38.zip && unzip Trimmomatic-0.38.zip