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Dockerfile
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####################################################################################
######## This is a Dockerfile with minimal set of #########
######## dependencies for running only smCounter-v2 #########
####################################################################################
# Using a biocontainer base image
# Please see below for further details :
# https://github.com/BioContainers/containers/blob/master/biocontainers/1.1.0/Dockerfile
FROM biocontainers/biocontainers:v1.1.0_cv1
MAINTAINER Raghavendra Padmanabhan <raghavendra.padmanabhan@qiagen.com>
################ Create appropriate directory structure for code to run ################
USER root
RUN mkdir -p /srv/qgen/code && \
mkdir -p /srv/qgen/bin/downloads
################ Update package repository and install dependencies using apt-get ################
RUN apt-get -y update && \
apt-get -y install r-base libcurl4-openssl-dev libssl-dev libxml2-dev && \
apt-get clean && apt-get purge && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
################ Install various version specific 3rd party tools ################
RUN conda install bedtools=2.25.0
################ Install python modules ################
## Install some modules with conda
RUN conda install scipy pysam=0.9.0
################ R packages ################
RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
RUN Rscript -e "install.packages(c('plyr','tidyverse','magrittr','data.table'))"
################ Update Environment Variables ################
ENV PYTHONPATH $PYTHONPATH:/opt/conda/lib/python2.7/site-packages/:/srv/qgen/code/qiaseq-dna/