https://github.com/amlalejini/directed-digital-evolution
Tip revision: c94684a751a54bc6f2ef2e7c0830614dc280ca01 authored by Alexander Lalejini on 29 June 2022, 17:30:58 UTC
add sample size section to supplemental toc
add sample size section to supplemental toc
Tip revision: c94684a
Dockerfile
# ======= USAGE =======
# Run interactively:
# docker run -it --entrypoint bash dockertest:latest
# Pull a base image
FROM ubuntu:20.04
COPY . /opt/directed-digital-evolution
# To make installs not ask questions about timezones
ARG DEBIAN_FRONTEND=noninteractive
ENV TZ=America/New_York
##############################
# install base dependencies
# - for R repository
# - dirmngr
# - gpg-agent
# - for bookdown compilation
# - pandoc, pandoc-citeproc, texlive-base, texlive-latex-extra
##############################
RUN \
apt-get update \
&& \
apt-get install -y -qq --no-install-recommends \
software-properties-common \
curl \
g++-10 \
make \
cmake \
python3 \
python3-pip \
python3-virtualenv \
git \
libssl-dev \
libcurl4-openssl-dev \
libxml2-dev \
libz-dev \
libgit2-dev \
libpng-dev \
libfontconfig1-dev \
libmagick++-dev \
libgdal-dev \
libharfbuzz-dev \
libfribidi-dev \
liblapack-dev \
libblas-dev \
libstdc++-10-dev \
dirmngr \
gpg-agent \
pandoc \
pandoc-citeproc \
texlive-base \
texlive-latex-extra \
lmodern \
&& \
echo "installed base dependencies"
# Wire g++ command to g++-10
RUN cd /usr/bin/ && ln -s g++-10 g++ && cd /
RUN \
pip3 install -r /opt/directed-digital-evolution/experiments/requirements.txt \
&& \
pip3 install osfclient \
&& \
echo "installed python requirements"
# Init & update git submodules
RUN \
cd /opt/directed-digital-evolution \
&& \
git submodule update --init --recursive \
&& \
echo "download git submodules"
# Build experiment
RUN \
cd /opt/directed-digital-evolution \
&& \
./build_exps.sh \
&& \
echo "build experiment software"
########################################################
# install r
# - source: https://rtask.thinkr.fr/installation-of-r-4-0-on-ubuntu-20-04-lts-and-tips-for-spatial-packages/
########################################################
RUN \
gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
&& \
gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9 | apt-key add - \
&& \
apt update \
&& \
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' \
&& \
apt-get install -y -q --no-install-recommends \
r-base \
r-base-dev \
libssl-dev \
libcurl4-openssl-dev \
libfreetype6-dev \
libmagick++-dev \
libxml2-dev \
libfontconfig1-dev \
cargo \
&& \
R -e "install.packages('rmarkdown', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('knitr', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('bookdown', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('tidyverse', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('cowplot', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('plyr', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('scales', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('RColorBrewer', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
R -e "install.packages('khroma', dependencies=NA, repos='http://cran.rstudio.com/')" \
&& \
echo "installed r and configured r environment"
########################################################
# download data needed to compile supplement
########################################################
RUN \
export OSF_PROJECT=zn63x \
&& \
export PROJECT_PATH=/opt/directed-digital-evolution \
&& \
cd ${PROJECT_PATH} \
&& \
export EXP_TAG=2021-11-15-ec \
&& \
./download_data.sh \
&& \
export EXP_TAG=2021-11-11-selection \
&& \
./download_data.sh \
&& \
export EXP_TAG=2021-11-30-aligned-tasks \
&& \
./download_data.sh \
&& \
export EXP_TAG=2021-11-12-time \
&& \
./download_data.sh \
&& \
export EXP_TAG=2021-11-16-pops \
&& \
./download_data.sh \
&& \
export EXP_TAG=2021-11-08-longer-genomes \
&& \
./download_data.sh \
&& \
export EXP_TAG=2021-09-30-sample-size \
&& \
./download_data.sh \
&& \
echo "downloaded experiment data"
########################################################
# build supplemental material (will also run data analyses)
########################################################
RUN \
cd /opt/directed-digital-evolution/ \
&& \
./build_book.sh \
&& \
echo "ran analyses and built supplemental material"
# Define default working directory.
WORKDIR /opt/directed-digital-evolution