Dockerfile

#################################################################
# Dockerfile
#
# Description:      Docker container with BWA-0.7.15 | samtools-1.3 | sambamba-0.6.3 | varscan-2.4.2 | samblaster-0.1.22 | abra-0.97 | vcftools-0.1.14 | vcflib-1.0.0-rc1 to call variants from deep sequencing (CAPP-Seq) data.
# Base Image:       ubuntu
# Pull Cmd:         docker pull anu9109/capp-seq
# Run Cmd:          docker run -it anu9109/capp-seq
# Run tools as:     docker run -it anu9109/capp-seq bwa 
#		    docker run -it anu9109/capp-seq samtools 
#		    docker run -it anu9109/capp-seq sambamba 
#		    docker run -it anu9109/capp-seq java -jar /opt/software/varscan/VarScan.v2.4.2.jar
#		    docker run -it anu9109/capp-seq samblaster
#	    	    docker run -it anu9109/capp-seq vcftools
#		    docker run -it anu9109/capp-seq vcfcombine (or any vcflib command)
#		    docker run -it anu9109/capp-seq java -jar /opt/software/abra.jar
#################################################################

# Set the base image to Ubuntu
FROM ubuntu

################## BEGIN INSTALLATION ###########################

ARG DEBIAN_FRONTEND=noninteractive

RUN apt-get update && \
  apt-get install -y \
  git \
  autoconf \
  curl \
  gcc \
  make \
  gawk \
  g++ \
  perl \
  pkg-config \ 
  zlib1g-dev \
  wget \
  libncurses5-dev \
  libcurl4-gnutls-dev \
  libgnutls-dev \
  libssl-dev \
  libexpat1-dev \
  libgd-gd2-perl \
  cpanminus \
  build-essential \
  libgd-dev \
  nettle-dev \
  bioperl \
  r-base \
  r-base-dev \
  r-cran-xml \
  libxml2-dev \
  default-jre \ 
  default-jdk && \
  apt-get clean && \
  apt-get purge && \
  rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*


# create /opt/software
RUN mkdir -p /opt/software

# install BWA-0.7.15
RUN cd /opt/software/ && \
  wget https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2 && \
  tar -xvjf /opt/software/bwa-0.7.15.tar.bz2 && \
  cd /opt/software/bwa-0.7.15 && \
  make && \
  rm /opt/software/bwa-0.7.15.tar.bz2

# install samtools-1.3
RUN cd /opt/software/ && \
  wget https://github.com/samtools/samtools/releases/download/1.3/samtools-1.3.tar.bz2 && \
  tar -xvjf /opt/software/samtools-1.3.tar.bz2 && \
  cd /opt/software/samtools-1.3 && \
  make && \
  make install
RUN cd /opt/software/samtools-1.3/htslib-1.3 && \
  ./configure && \
  make && \
  make install && \
  rm /opt/software/samtools-1.3.tar.bz2

# install sambamba-0.6.3
RUN cd /opt/software/ && \
  wget https://github.com/lomereiter/sambamba/releases/download/v0.6.3/sambamba_v0.6.3_linux.tar.bz2 && \
  tar -xvjf sambamba_v0.6.3_linux.tar.bz2 && \
  mv /opt/software/sambamba_v0.6.3 /opt/software/sambamba && \
  rm /opt/software/sambamba_v0.6.3_linux.tar.bz2

# install varscan-2.4.2 
RUN cd /opt/software/ && \
  git clone https://github.com/dkoboldt/varscan.git 

# install vcftools-0.1.14
RUN  cd /opt/software/ && \
  git clone https://github.com/vcftools/vcftools.git && \
  cd /opt/software/vcftools && \
  ./autogen.sh && \
  ./configure && \
  make && \
  make install

# install vcflib-1.0.0-rc1
RUN  cd /opt/software/ && \
  git clone --recursive https://github.com/vcflib/vcflib.git && \
  cd /opt/software/vcflib && \
  make openmp

# install abra-0.97
RUN  cd /opt/software/ && \
  wget https://github.com/mozack/abra/releases/download/v0.97/abra-0.97-SNAPSHOT-jar-with-dependencies.jar && \
  mv /opt/software/abra-0.97-SNAPSHOT-jar-with-dependencies.jar /opt/software/abra.jar

# install samblaster-0.1.22
RUN  cd /opt/software/ && \
  git clone git://github.com/GregoryFaust/samblaster.git && \
  cd /opt/software/samblaster && \
  make

# install R packages
RUN wget https://cran.r-project.org/src/base/R-3/R-3.3.0.tar.gz && tar -zxvf R-3.3.0.tar.gz && cd R-3.3.0 && ./configure && make && make install && rm -r /R-3.3.0.tar.gz
RUN echo "local({r <- getOption('repos'); r['CRAN'] <- 'https://cran.cnr.berkeley.edu'; options(repos=r)})" > ~/.Rprofile
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' \ 
  -e 'biocLite("Rsamtools")' \
  -e 'biocLite("VariantAnnotation")' \
  -e 'biocLite("GenomicRanges")'
RUN Rscript  -e 'install.packages("plyr")'
RUN Rscript -e "install.packages('optparse')"

# adding contamination check script and panel
#RUN mkdir -p /home/cont
#ADD cont.R /home/cont/
#ADD contPanel.csv /home/cont/

ENV PATH=$PATH:/opt/software:/opt/software/varscan:/opt/software/vcflib/bin:/opt/software/samblaster:/opt/software/samtools-1.3/htslib-1.3


##################### INSTALLATION END ##########################

# File Author / Maintainer
MAINTAINER Anu Amallraja <anu9109@gmail.com>