Dockerfile_commet_galaxy.txt

############################################################
# Dockerfile to build Commet tool container image for Galaxy
# Based on debian wheezy
############################################################

# Set the base image to debian wheezy
FROM debian:wheezy

# Set noninterative mode
ENV DEBIAN_FRONTEND noninteractive
ENV PACKAGES wget make gcc g++ unzip curl r-base python

ENV ZIP http://github.com/pierrepeterlongo/commet/archive/master.zip
ENV SOURCE commet-master
ENV DIR /opt

################## DEPENDENCIES INSTALLATION ######################

RUN apt-get update -y
RUN apt-get install -y ${PACKAGES}


#################### INSTALL GPLOTS FOR R  #########################

RUN curl -O http://cran.ma.imperial.ac.uk/src/contrib/Archive/gplots/gplots_2.6.0.tar.gz
RUN tar xzf gplots_2.6.0.tar.gz

RUN echo 'options(repos=structure(c(CRAN="http://cran.ma.imperial.ac.uk")))' > /tmp/inst.sh
RUN echo 'install.packages("gtools")' >> /tmp/inst.sh
RUN echo 'install.packages("gdata")' >> /tmp/inst.sh
RUN echo 'install.packages("gplots", repos = NULL, type="source")' >> /tmp/inst.sh

RUN Rscript /tmp/inst.sh

################## COMMET INSTALLATION ######################

WORKDIR ${DIR}
ADD ${ZIP} tmp.zip
RUN unzip tmp.zip && rm tmp.zip
WORKDIR ${DIR}/${SOURCE}
RUN make && make install
ENV RSCRIPTS ${DIR}/${SOURCE}
ENV BINARIES ${DIR}/${SOURCE}/bin/
#ENTRYPOINT ["./commet.py"]
#CMD ["-h"]

ADD commet.py /usr/local/bin/commet.py
RUN chmod 755 /usr/local/bin/commet.py

##################### Maintainer #####################

MAINTAINER Le Bras Yvan <le_bras.yvan@irisa.fr>

#################### Example ########################
# docker run -it --rm cmonjeau/commet
# docker run -it --rm -v /root/Commet:/data cmonjeau/commet /data/sets_config.txt -k 33 -o /data/results