Dockerfile

# PhenoMeNal H2020
# Microservices - IPO
FROM container-registry.phenomenal-h2020.eu/phnmnl/xcms

MAINTAINER PhenoMeNal-H2020 Project ( phenomenal-h2020-users@googlegroups.com )

LABEL software=IPO
LABEL software.version=1.4.1
LABEL version=0.8
LABEL base.image="container-registry.phenomenal-h2020.eu/phnmnl/xcms"
LABEL description="A Tool for automated Optimization of XCMS Parameters"
LABEL website="https://github.com/phnmnl/container-ipo"
LABEL documentation="https://github.com/phnmnl/container-ipo"
LABEL license="https://github.com/phnmnl/container-ipo/blob/develop/LICENSE"
LABEL tags="Metabolomics"

# Add IPO scripts and W4M wrapper to path
COPY scripts/* /usr/local/bin/

# Install dependencies
######
# The installation with github "grimbough/Rhdf5lib" can be deleted when R 3.5.0 will be available. 
# Rhdf5lib >= 1.1.4 is required by 'sneumann-mzR-4f83846'
######
RUN apt-get update && apt-get install -y --no-install-recommends \
      wget \
      ca-certificates \
      make \
      gcc \
      gfortran \
      g++ \
      r-base-dev \
      libblas-dev \
      liblapack-dev \
      libboost-dev \
      libcurl4-openssl-dev \
      libssl-dev \
      libssh2-1-dev \
      libxml2-utils \
      icu-devtools \
      netcdf-bin && \
    echo 'options("repos"="http://cran.rstudio.com")' >> /etc/R/Rprofile.site && \
    R -e 'install.packages("devtools"); library("devtools"); install_github("grimbough/Rhdf5lib"); install_github("sneumann/mzR"); install.packages(c("batch", "rsm"))' && \
    R -e 'source("https://bioconductor.org/biocLite.R"); biocLite("IPO");' && \
    apt-get --purge -y --auto-remove remove make gcc gfortran g++ libcurl4-openssl-dev libssl-dev libssh2-1-dev libboost-dev && \
	  apt-get clean && apt-get autoremove -y && rm -rf /var/lib/apt/lists/* /var/lib/{cache,log}/ /tmp/* /var/tmp/*

# Add testing to container
COPY runTest1.sh /usr/local/bin/runTest1.sh

# Define Entry point script (Warning: may break Galaxy scripts!)
#ENTRYPOINT ["runIPO.R"]