New source image. #12
|
@ -0,0 +1,14 @@
|
|||
#!/usr/bin/with-contenv bash
|
||||
# shellcheck shell=bash
|
||||
|
||||
## Set our dynamic variables in Renviron.site to be reflected by RStudio Server or Shiny Server
|
||||
exclude_vars="HOME PASSWORD RSTUDIO_VERSION BATCH_USER_CREATION"
|
||||
for file in /var/run/s6/container_environment/*
|
||||
do
|
||||
sed -i "/^${file##*/}=/d" ${R_HOME}/etc/Renviron.site
|
||||
regex="(^| )${file##*/}($| )"
|
||||
[[ ! $exclude_vars =~ $regex ]] && echo "${file##*/}=$(cat $file)" >> ${R_HOME}/etc/Renviron.site || echo "skipping $file"
|
||||
done
|
||||
|
||||
## only file-owner (root) should read container_environment files:
|
||||
chmod 600 /var/run/s6/container_environment/*
|
|
@ -0,0 +1,118 @@
|
|||
#!/usr/bin/with-contenv bash
|
||||
# shellcheck shell=bash
|
||||
|
||||
## Set defaults for environmental variables in case they are undefined
|
||||
DEFAULT_USER=${DEFAULT_USER:-rstudio}
|
||||
USER=${USER:=${DEFAULT_USER}}
|
||||
USERID=${USERID:=1000}
|
||||
GROUPID=${GROUPID:=1000}
|
||||
ROOT=${ROOT:=FALSE}
|
||||
UMASK=${UMASK:=022}
|
||||
LANG=${LANG:=en_US.UTF-8}
|
||||
TZ=${TZ:=Etc/UTC}
|
||||
HOME=/home/${USER}
|
||||
|
||||
bold=$(tput bold)
|
||||
normal=$(tput sgr0)
|
||||
|
||||
if [[ ${DISABLE_AUTH,,} == "true" ]]
|
||||
|
||||
then
|
||||
mv /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
|
||||
echo "USER=$USER" >> /etc/environment
|
||||
fi
|
||||
|
||||
if grep --quiet "auth-none=1" /etc/rstudio/rserver.conf
|
||||
then
|
||||
echo "Skipping authentication as requested"
|
||||
elif [ -z "$PASSWORD" ]
|
||||
then
|
||||
PASSWORD=$(pwgen 16 1)
|
||||
printf "\n\n"
|
||||
tput bold
|
||||
printf "The password is set to \e[31m%s\e[39m\n" "$PASSWORD"
|
||||
printf "If you want to set your own password, set the PASSWORD environment variable. e.g. run with:\n"
|
||||
printf "docker run -e PASSWORD=\e[92m<YOUR_PASS>\e[39m -p 8787:8787 rocker/rstudio\n"
|
||||
tput sgr0
|
||||
printf "\n\n"
|
||||
fi
|
||||
|
||||
if [ "$USERID" -lt 1000 ]
|
||||
# Probably a macOS user, https://github.com/rocker-org/rocker/issues/205
|
||||
then
|
||||
echo "$USERID is less than 1000"
|
||||
check_user_id=$(grep -F "auth-minimum-user-id" /etc/rstudio/rserver.conf)
|
||||
if [[ ! -z $check_user_id ]]
|
||||
then
|
||||
echo "minumum authorised user already exists in /etc/rstudio/rserver.conf: $check_user_id"
|
||||
else
|
||||
echo "setting minumum authorised user to 499"
|
||||
echo auth-minimum-user-id=499 >> /etc/rstudio/rserver.conf
|
||||
fi
|
||||
fi
|
||||
|
||||
if [ "$USERID" -ne 1000 ]
|
||||
## Configure user with a different USERID if requested.
|
||||
then
|
||||
echo "deleting the default user"
|
||||
userdel $DEFAULT_USER
|
||||
echo "creating new $USER with UID $USERID"
|
||||
useradd -m $USER -u $USERID
|
||||
mkdir -p /home/$USER
|
||||
chown -R $USER /home/$USER
|
||||
usermod -a -G staff $USER
|
||||
elif [ "$USER" != "$DEFAULT_USER" ]
|
||||
then
|
||||
## cannot move home folder when it's a shared volume, have to copy and change permissions instead
|
||||
cp -r /home/$DEFAULT_USER/* /home/$USER
|
||||
cp -r /home/$DEFAULT_USER/.??* /home/$USER
|
||||
## RENAME the user
|
||||
usermod -l $USER -d /home/$USER $DEFAULT_USER
|
||||
groupmod -n $USER $DEFAULT_USER
|
||||
usermod -a -G staff $USER
|
||||
chown -R $USER:$USER /home/$USER
|
||||
echo "USER is now $USER"
|
||||
fi
|
||||
|
||||
[ "$USER" != "rstudio" ] && rm -fr /home/rstudio
|
||||
|
||||
if [ "$GROUPID" -ne 1000 ]
|
||||
## Configure the primary GID (whether rstudio or $USER) with a different GROUPID if requested.
|
||||
then
|
||||
echo "Modifying primary group $(id $USER -g -n)"
|
||||
groupmod -g $GROUPID $(id $USER -g -n)
|
||||
echo "Primary group ID is now custom_group $GROUPID"
|
||||
fi
|
||||
|
||||
if [[ ${DISABLE_AUTH,,} != "true" ]]
|
||||
then
|
||||
## Add a password to user
|
||||
echo "$USER:$PASSWORD" | chpasswd
|
||||
fi
|
||||
|
||||
# Use Env flag to know if user should be added to sudoers
|
||||
if [[ ${ROOT,,} == "true" ]]
|
||||
then
|
||||
adduser $USER sudo && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
|
||||
echo "$USER added to sudoers"
|
||||
fi
|
||||
|
||||
## Change Umask value if desired
|
||||
if [ "$UMASK" -ne 022 ]
|
||||
then
|
||||
echo "server-set-umask=false" >> /etc/rstudio/rserver.conf
|
||||
echo "Sys.umask(mode=$UMASK)" >> /home/$USER/.Rprofile
|
||||
fi
|
||||
|
||||
## Next one for timezone setup
|
||||
if [ "$TZ" != "Etc/UTC" ]
|
||||
then
|
||||
ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
|
||||
fi
|
||||
|
||||
## Update Locale if needed
|
||||
if [ "$LANG" != "en_US.UTF-8" ]
|
||||
then
|
||||
/usr/sbin/locale-gen --lang $LANG
|
||||
/usr/sbin/update-locale --reset LANG=$LANG
|
||||
fi
|
60
Dockerfile
60
Dockerfile
|
@ -1,9 +1,5 @@
|
|||
FROM rocker/r-ver:4.1.3
|
||||
FROM d4science/r-full:latest
|
||||
|
||||
LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
|
||||
org.opencontainers.image.source="https://github.com/rocker-org/rocker-versioned2" \
|
||||
org.opencontainers.image.vendor="Rocker Project" \
|
||||
org.opencontainers.image.authors="Carl Boettiger <cboettig@ropensci.org>"
|
||||
|
||||
ENV S6_VERSION=v2.1.0.2
|
||||
ENV RSTUDIO_VERSION=2022.02.1+461
|
||||
|
@ -11,52 +7,6 @@ ENV DEFAULT_USER=rstudio
|
|||
ENV PANDOC_VERSION=default
|
||||
ENV PATH=/usr/lib/rstudio-server/bin:$PATH
|
||||
|
||||
# Install OpenJDK
|
||||
RUN apt-get update && apt-get install -y openjdk-8-jdk-headless openjdk-8-jre-headless
|
||||
|
||||
# Some R dependencies
|
||||
RUN apt-get update && apt-get install -y \
|
||||
libxml2 \
|
||||
git \
|
||||
gdal-bin \
|
||||
netcdf-bin \
|
||||
sshpass \
|
||||
p7zip-full \
|
||||
sox \
|
||||
imagemagick \
|
||||
proj-bin \
|
||||
proj-data \
|
||||
libgsl23 \
|
||||
postgresql-server-dev-all \
|
||||
libsecret-1-0
|
||||
|
||||
# Install the R packages we need, using the binary distribution
|
||||
# at https://packagemanager.rstudio.com/client/#/repos/1/overview
|
||||
ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/install2r-packages.txt /tmp
|
||||
RUN for f in `cat /tmp/install2r-packages.txt` ; do install2.r --error --skipinstalled --ncpus -1 $f ; done
|
||||
|
||||
# Non CRAN repositories
|
||||
ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_non_cran_pkgs.txt /tmp
|
||||
RUN for l in `cat /tmp/r_non_cran_pkgs.txt` ; do \
|
||||
pkg=`echo $l | cut -d : -f 1` ; \
|
||||
mirror=`echo $l | cut -d : -f 2-` ; \
|
||||
Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
|
||||
-e "install.packages(pkgs='$pkg', repos=c('$mirror/'));" ; done
|
||||
|
||||
# From github
|
||||
ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_github_pkgs.txt /tmp
|
||||
RUN mkdir -p /etc/R
|
||||
#RUN echo "GITHUB_PAT=$GITHUB_PAT" >> /etc/R/Renviron.site
|
||||
#RUN for g in `cat /tmp/r_github_pkgs.txt` ; do \
|
||||
# Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
|
||||
# -e " require(devtools); devtools::install_github('$g')" ; done
|
||||
#RUN for g in `cat /tmp/r_github_pkgs.txt` ; do installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest $g ; done
|
||||
#RUN grep -v "GITHUB_PATH" /etc/R/Renviron.site > /etc/R/Renviron.site.1
|
||||
#RUN mv -f /etc/R/Renviron.site.1 /etc/R/Renviron.site
|
||||
RUN installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest DanOvando/sraplus
|
||||
|
||||
# Ensure that we remove the source packages
|
||||
RUN rm -fr /tmp/downloaded_packages/*
|
||||
|
||||
RUN /rocker_scripts/install_rstudio.sh
|
||||
RUN /rocker_scripts/install_pandoc.sh
|
||||
|
@ -68,12 +18,14 @@ RUN mkdir /workspace
|
|||
RUN echo "www-frame-origin=same" >> /etc/rstudio/disable_auth_rserver.conf
|
||||
RUN echo "www-verify-user-agent=0" >> /etc/rstudio/disable_auth_rserver.conf
|
||||
|
||||
ADD 03_setup_root_path.sh /etc/cont-init.d/03_setup_root_path.sh
|
||||
ADD 01_set_env.sh /etc/cont-init.d/01_set_env
|
||||
ADD 02_userconf.sh /etc/cont-init.d/02_userconf
|
||||
ADD 03_setup_root_path.sh /etc/cont-init.d/03_setup_root_path
|
||||
|
||||
# By default RStudio does not give access to all enviornment variables defined in the container (e.g. using ShinyProxy).
|
||||
# Uncomment the next line, to change this behavior.
|
||||
#ADD 04_copy_env.sh /etc/cont-init.d/04_copy_env.sh
|
||||
ADD 05_setup_rsession_parameters.sh /etc/cont-init.d/05_setup_rsession_parameters.sh
|
||||
#ADD 04_copy_env.sh /etc/cont-init.d/04_copy_env
|
||||
ADD 05_setup_rsession_parameters.sh /etc/cont-init.d/05_setup_rsession_parameters
|
||||
|
||||
EXPOSE 8787
|
||||
|
||||
|
|
Loading…
Reference in New Issue