If I create a dockerfile based on Debian I can add the following line to execute a script when I'm initiating the container:
COPY userconf.sh /etc/cont-init.d/userconf
What would be the equivalent with for a dockerfile based on Ubuntu 16.04? In case it is relevant, this is the script that I want to run.
I tried implementing the changes that @A.B. recommended but things are still not working. This is my dockerfile:
FROM r-gpu
ARG RSTUDIO_VERSION
## Comment the next line to use the latest RStudio Server version by default
#ENV RSTUDIO_VERSION=${RSTUDIO_VERSION:-1.1.447}
ENV PATH=/usr/lib/rstudio-server/bin:$PATH
## Download and install RStudio server & dependencies
## Attempts to get detect latest version, otherwise falls back to version given in $VER
## Symlink pandoc, pandoc-citeproc so they are available system-wide
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
git \
libedit2 \
psmisc \
python-setuptools \
sudo \
wget \
&& RSTUDIO_LATEST=$(wget --no-check-certificate -qO- https://s3.amazonaws.com/rstudio-server/current.ver) \
&& [ -z "$RSTUDIO_VERSION" ] && RSTUDIO_VERSION=$RSTUDIO_LATEST || true \
&& wget -q http://download2.rstudio.org/rstudio-server-${RSTUDIO_VERSION}-amd64.deb \
&& dpkg -i rstudio-server-${RSTUDIO_VERSION}-amd64.deb \
&& rm rstudio-server-*-amd64.deb \
## Symlink pandoc & standard pandoc templates for use system-wide
&& ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc /usr/local/bin \
&& ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc /usr/local/bin \
&& git clone https://github.com/jgm/pandoc-templates \
&& mkdir -p /opt/pandoc/templates \
&& cp -r pandoc-templates*/* /opt/pandoc/templates && rm -rf pandoc-templates* \
&& mkdir /root/.pandoc && ln -s /opt/pandoc/templates /root/.pandoc/templates \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/ \
&& mkdir -p /usr/local/lib/R/etc \
## RStudio wants an /etc/R, will populate from $R_HOME/etc
&& mkdir -p /etc/R \
## Write config files in $R_HOME/etc
&& echo '\n\
\n# Configure httr to perform out-of-band authentication if HTTR_LOCALHOST \
\n# is not set since a redirect to localhost may not work depending upon \
\n# where this Docker container is running. \
\nif(is.na(Sys.getenv("HTTR_LOCALHOST", unset=NA))) { \
\n options(httr_oob_default = TRUE) \
\n}' >> /usr/local/lib/R/etc/Rprofile.site \
&& echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron \
## Prevent rstudio from deciding to use /usr/bin/R if a user apt-get installs a package
&& echo 'rsession-which-r=/usr/local/bin/R' >> /etc/rstudio/rserver.conf \
## use more robust file locking to avoid errors when using shared volumes:
&& echo 'lock-type=advisory' >> /etc/rstudio/file-locks \
## configure git not to request password each time
&& git config --system credential.helper 'cache --timeout=3600' \
&& git config --system push.default simple \
## Set up S6 init system
&& wget -P /tmp/ https://github.com/just-containers/s6-overlay/releases/download/v1.11.0.1/s6-overlay-amd64.tar.gz \
&& tar xzf /tmp/s6-overlay-amd64.tar.gz -C / \
&& mkdir -p /etc/services.d/rstudio \
&& echo '#!/usr/bin/with-contenv bash \
\n exec /usr/lib/rstudio-server/bin/rserver --server-daemonize 0' \
> /etc/services.d/rstudio/run \
&& echo '#!/bin/bash \
\n rstudio-server stop' \
> /etc/services.d/rstudio/finish
COPY userconf.sh /usr/local/bin/userconf.sh
## running with "-e ADD=shiny" adds shiny server
COPY add_shiny.sh /usr/local/bin/add_shiny.sh
COPY pam-helper.sh /usr/local/bin/pam-helper.sh
COPY start.sh /usr/local/bin/start.sh
RUN ln /usr/bin/R /usr/local/bin/R
EXPOSE 8787
CMD ["/bin/bash", "/usr/local/bin/start.sh"]
This is the userconf.sh :
#!/usr/bin/env bash
## Set defaults for environmental variables in case they are undefined
USER=${USER:=rstudio}
PASSWORD=${PASSWORD:=rstudio}
USERID=${USERID:=1000}
GROUPID=${GROUPID:=1000}
ROOT=${ROOT:=FALSE}
UMASK=${UMASK:=022}
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 user rstudio"
userdel rstudio
echo "creating new $USER with UID $USERID"
useradd -m $USER -u $USERID
mkdir /home/$USER
chown -R $USER /home/$USER
usermod -a -G staff $USER
elif [ "$USER" != "rstudio" ]
then
## cannot move home folder when it's a shared volume, have to copy and change permissions instead
cp -r /home/rstudio /home/$USER
## RENAME the user
usermod -l $USER -d /home/$USER rstudio
groupmod -n $USER rstudio
usermod -a -G staff $USER
chown -R $USER:$USER /home/$USER
echo "USER is now $USER"
fi
if [ "$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 $GROUPID"
fi
## Add a password to user
echo "$USER:$PASSWORD" | chpasswd
# Use Env flag to know if user should be added to sudoers
if [ "$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/$USER/.Rprofile
fi
## add these to the global environment so they are avialable to the RStudio user
echo "HTTR_LOCALHOST=$HTTR_LOCALHOST" >> /etc/R/Renviron.site
echo "HTTR_PORT=$HTTR_PORT" >> /etc/R/Renviron.site
and this is the start.sh
#!/usr/bin/env bash
/usr/local/bin/userconf.sh
/usr/local/bin/add_shiny.sh
/usr/local/bin/pam-helper.sh
exec /usr/lib/rstudio-server/bin/rserver --server-daemonize=0 --server-app-armor-enabled=0
What am I missing?
