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#########################################################################################
#
# Docker file for Simka project.
#
# It prepares a Docker container to run Simka jobs:
#
# - bin/simka: computing simka results from sequencing data
# - scripts/visualization/run-visualization.py: making images from results of
# bin/simka.
#
#########################################################################################
#
# == Docker build command:
#
# docker build -f Dockerfile -t simka_machine .
#
# == Docker test command:
#
# docker run --rm -i -t simka_machine -c test
#
# -> you should see a simka test with some provided data.
#
# == Running a Simka job:
#
# docker run --rm -i -t simka_machine -c <command> -- <args>
#
# where:
# <command>: MUST BE one of: simka, visu, test
# <arguments>: remaining arguments passed in after <command> are passed
# to the appropriate simka program:
# - simka: will run 'bin/simka' within the container
# - visu: will run 'scripts/visualization/run-visualization.py'
# within the container
# Please refer to these programs to review their expected arguments.
# See https://github.com/GATB/simka
#
# == Sample Simka job with provided data:
#
# docker run --rm -i -t -v $PWD:/tmp simka_machine -c simka -- -in /opt/simka/example/simka_input.txt -out /tmp/simka_results/ -out-tmp /tmp/simka_temp_output
#
# -> you should have results in $PWD/simka_results directory when Simka job is done.
#
# This command-line line explained:
#
# docker run [1]
# --rm [2]
# -i -t [3]
# -v $PWD:/tmp [4]
# simka_machine [5]
# -c simka [6]
# -- [7]
# -in /opt/simka/example/simka_input.txt [8]
# -out /tmp/simka_results/ [9]
# -out-tmp /tmp/simka_temp_output [10]
#
# [1]-[5]: Docker arguments
# [6]-[7]: simka container's invoker program
# [8]-[10]: 'bin/simka' arguments
#
# [1]: start Docker container
# [2]: destroy container when Docker finishes
# (it does NOT delete the 'simka_machine' image)
# [3]: start an interactive job
# (for instance, you'll see messages on stdout, if any)
# [4]: mount a volume. This is required to get the results from Simka.
# Here, we say that current local directory will be viewed as '/tmp'
# from the inside of the container.
# [5]: tell Docker which image to start: the 'simka_machine' of course.
# [6]: ask to start the simka program. Other option is to start the
# 'visu' task (see below). See companion file 'run_simka.sh' for
# more information.
# [7]: '--' is required to separate arguments [6] from the rest of the
# command line
# [8]: the data file to process with simka. Here we use a data file
# provided with the simka software to test it.
# [9]: tells simka where to put results. Of course, simka will write
# within /tmp directory inside the container. However, since we
# have directive [4], data writing is actually done in $PWD, i.e.
# a local directory.
# [10]: tells simka where to put temporary files.
#
# == Sample Simka Visualization job with provided data
#
# After running the previous command, you can do this:
#
# docker run --rm -i -t -v $PWD:/tmp simka_machine -c visu -- -in /tmp/simka_results/ -out /tmp/simka_results/ -pca -heatmap -tree
#
# -> you should have PNG files in $PWD/simka_results directory.
#
# == Additional notes
#
# Root access inside the container:
#
# - if running: docker exec -it simka_machine bash
#
# - if not yet running: docker run --rm -i -t simka_machine bash
#
#########################################################################################
# Simka binary available on Github (see below) is built using a
# Debian 8 (jessie) based system on Inria Jenkins CI platform
FROM debian:jessie
# who to blame?
MAINTAINER Patrick Durand patrick.durand@inria.fr
# ###
# We always use the latest official SIMKA release.
#
ENV SIMKA_VERSION=1.4.0
# ###
# Package installation and configuration
#
RUN apt-get update && apt-get -y dist-upgrade \
&& apt-get install -y --no-install-recommends curl python2.7 r-base \
&& apt-get clean
# ###
# SIMKA installation: get the binary release from Github mirror.
#
RUN cd /opt \
&& export SIMKA_TGZ=simka-v${SIMKA_VERSION}-bin-Linux.tar.gz \
&& export GIT_URL=https://github.com/GATB/simka/releases/download \
&& export SIMKA_URL=${GIT_URL}/v${SIMKA_VERSION}/${SIMKA_TGZ} \
&& curl -ksL ${SIMKA_URL} | tar xz \
&& rm -f ${SIMKA_TGZ} \
&& mv simka-v${SIMKA_VERSION}-bin-Linux simka \
&& cd simka/bin \
&& chmod +x simka* \
&& cd ../example \
&& chmod +x *.sh \
&& ./simple_test.sh
COPY run_simka.sh /opt/simka
# Fix: ensure script has exec permission
RUN chmod +x /opt/simka/run_simka.sh
# ###
# Start simka.
#
ENTRYPOINT ["/opt/simka/run_simka.sh"]
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