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/userconfWhat 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- ) \ && [ -z "$RSTUDIO_VERSION" ] && RSTUDIO_VERSION=$RSTUDIO_LATEST || true \ && wget -q \ && 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 \ && 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/ \ && 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 [ "$USERID" -lt 1000 ]
# Probably a macOS user, then echo "$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.siteand 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=0What am I missing?
1 Answer
Replace the line
#!/usr/bin/with-contenv bashwith
#!/usr/bin/env bashUbuntu doesn't know
/usr/bin/with-contenv.Use a
Dockerfilelike thisFROM ubuntu:16.04 […] COPY userconf.sh /usr/local/bin/userconf.sh COPY start.sh /usr/local/bin/start.sh […] CMD ["/bin/bash", "/usr/local/bin/start.sh"]Your
start.sh#!/usr/bin/env bash […] /usr/local/bin/userconf.sh […] exec your_script_to_start_a_foreground_process.sh
