get_phylomarkers/Dockerfile at master · MauriAndresMU1313/get_phylomarkers · GitHub

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## Dockerfile version 2021-09-20
# - build images using as context the freshly pulled get_phylomarkers GitHub repositor (or from git/get_phylomarkers)
# - now runs 22 tests during the final image's build stage & sets ENV R_LIBS_SITE
FROM ubuntu:18.04
FROM rstudio/r-base:3.6.3-bionic

LABEL authors="Pablo Vinuesa <https://www.ccg.unam.mx/~vinuesa/> and Bruno Contreras Moreira <https://www.eead.csic.es/compbio/>"
LABEL keywods="bioinformatics, genomics, phylogenetics, phylogenomics, core-genome, pan-genome, maximum likelihood, parsimony, population genetics, molecular clock, Docker image"
LABEL version="20210920"
LABEL description="Ubuntu 18.04 + rstudio/r-base:3.6.3-bionic based image of GET_PHYLOMARKERS"
LABEL summary="This image runs GET_PHYLOMARKERS for advanced and versatile phylogenomic analysis of microbial pan-genomes"
LABEL home="<https://hub.docker.com/r/vinuesa/get_phylomarkers>"
LABEL get_phylomarkers.github.home="<https://github.com/vinuesa/get_phylomarkers>"
LABEL get_phylomarkers.reference="PMID:29765358 <https://pubmed.ncbi.nlm.nih.gov/29765358/"
LABEL license="GPLv3 <https://www.gnu.org/licenses/gpl-3.0.html>"

## Install required linux tools
RUN apt-get update && apt-get install --no-install-recommends -y \
bash-completion \
bc \
build-essential \
cpanminus \
curl \
gcc \
libssl-dev \
make \
wget \
&& apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && cpanm Term::ReadLine

## mkdir get_phylomarkes in /, copy all contents into it; make it the working directory & install required R packages
RUN mkdir get_phylomarkers
COPY . /get_phylomarkers
WORKDIR /get_phylomarkers
RUN Rscript /get_phylomarkers/install_R_deps.R

# set R paths; run R -q -e '.libPaths()' on Linux (Ubuntu) host, and docker container;
ENV R_LIBS_SITE=/usr/local/lib/R/site-library:/usr/lib/R/site-library/:/usr/lib/R/library:/opt/R/3.6.3/lib/R/library:/get_phylomarkers/lib/R

## python2.7 required by paup; python2.7-dev to get libpython2.7.so.1.0
#   add python2.7 at this stage, as rstudio/r-base:3.6.3-bionic seems to overwrite�python2.7 in the first RUN apt-get above
#   this seems the only way to get python2.7 and python2.7-dev in newer ubuntu:18.04 images
#   as otherwise only python 3.6 gets installed.
#  Copy libnw required by newick-utils to /usr/local/lib and export LD_LIBRARY_PATH for ldconfig
RUN apt-get update && apt-get install --no-install-recommends -y python2.7 python2.7-dev \
&& apt-get clean && apt-get purge && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& cp /get_phylomarkers/lib/libnw.so /usr/local/lib \
&& export LD_LIBRARY_PATH=/usr/local/lib \
&& ldconfig \
&& chmod -R a+wr /get_phylomarkers/test_sequences

## add version tag to image
ARG version
LABEL version=$version
RUN echo $version

## Prepare USER env
RUN useradd --create-home --shell /bin/bash you
# set USER=you for pgrep calls, as the only ENV-VARS documented to be set are HOME HOSTNAME PATH and TERM
#  https://docs.docker.com/engine/reference/run/#env-environment-variables
ENV USER=you
USER you

# run get_phylomarkers tests on fully built image
RUN make clean && make test && make clean

WORKDIR /home/you
ENV PATH="${PATH}:/get_phylomarkers"

# make sure the user gets a Bash shell and some help to get started
CMD ["/bin/bash"]

## USAGE:
# 1. Copy test data from /get_phylomarkers/test_sequences
# - open a terminal on your post and type:
# $ cd && mkdir -p ~/data/genomes/test_sequences

# 2. Assuming that you have your core_genome and/or pan_genome data availabe in ~/data/genomes/test_sequences
# bind mount that host directory on the container instance under /home/you/data with the following command:
# $ docker run -it --rm -v ~/data/genomes/test_sequences:/home/you/data vinuesa/get_phylomarkers:latest /bin/bash

# Copy the test sequences to your data directory
# $ cp -r /get_phylomarkers/test_sequences/core_genome ~/data/
# $ cp -r /get_phylomarkers/test_sequences/pan_genome ~/data/
# $ cd ~/data

## Functional testing
# $ cd ~/data/core_genome
# $ ls
# $ run_get_phylomarkers_pipeline.sh -h
# $ run_get_phylomarkers_pipeline.sh -R 1 -t DNA
# $ cd ~/data/pan_genome
# $ estimate_pangenome_phylogenies.sh -f pangenome_matrix_t0.fasta -r 1 -S UFBoot

## Thorough functional testing (8 tests calling the two main scripts) can also be run automatically as follows,
#   assuming that you have copied the core_genome and pan_genome test sequences to the data directory, as indicated above.
# $ cd && run_test_suite.sh /home/you/data