singularity

singularity/README.md

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+## Singularity RStudio Server
+
+Image based on the Ubuntu 20.04 (R 4.2.2), see `./singularity/rstudio_server/recipe-4-2-2.def` for details
+
+### First step (get the image)
+
+Download the image at <https://cloud.sylabs.io/library/michael.rade/r-world/rstudio-server> or pull it:
+
+``` sh
+$ singularity pull --arch amd64 library://michael.rade/r-world/rstudio-server:1.0.0
+```
+
+### Second step (config and run)
+
+The following adjustments must be made in the `run.sh` file:
+
+-   Set a port (variable `RSTUDIO_PORT`)
+-   Set a path for the log files (variable `TMPDIR`)
+-   The variable `RSTUDIO_PASSWORD` can be set to a password of your choice. Default is "password"
+-   For parameter `auth-pam-helper` and `rsession-config-file` in run.sh: Set path to this folder.
+
+Furthermore, set your R library path in `./singularity/rsession.conf`. I recommend to create a new folder. It can lead to conflicts when folders with libraries of another R version are used.
+
+Now run the following :
+
+``` sh
+$ bash run.sh run rstudio-server:1.0.0.sif
+```
+
+You can reach RStudio Server via your webbrowser (e.g. `localhost:8072/auth-sign-in`). Use the port that you have specified in the variable `RSTUDIO_PORT`. You can log in with your current user name and password you set in `RSTUDIO_PASSWORD`.
+
+### Notes
+
+You can also work on the command line
+
+``` sh
+# If you need to bind something that is not your user's home directory
+$ export SINGULARITY_BINDPATH="/mnt/example/"
+# Define path to R libraries
+$ export R_LIBS_USER="/home//michael.rade/R/x86_64-pc-linux-gnu-library/4.0.2.RStudioServer/"
+
+$ singularity shell rstudio-server:1.0.0.sif
+$ R
+```
+
+You can build this singularity image with:
+
+``` sh
+$ sudo singularity build rstudio-server:1.0.0.sif recipe-4-2-2.def
+```
+
+You can put more parameter to run.sh. To see all possible parameter use:
+
+``` sh
+$ singularity run --app rserver rstudio-server_1.0.0.sif --help
+```

singularity/recipe-4-2-2.def

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+Bootstrap: docker
+From: ubuntu:20.04
+
+%labels
+  Maintainer Michael Rade
+  R_Version 4.2.2
+  RStudio_Version 2021.09.2-382
+
+%runscript
+  exec rserver "${@}"
+
+%apprun rserver
+  exec rserver "${@}"
+
+%environment
+  export PATH=/usr/lib/rstudio-server/bin:${PATH}
+
+%setup
+  install -Dv \
+    rstudio_auth.sh \
+    ${SINGULARITY_ROOTFS}/usr/lib/rstudio-server/bin/rstudio_auth
+
+%post
+  # Software versions
+  export R_VERSION=4.2.2
+  export RSTUDIO_VERSION=2021.09.2-382
+
+  # Get dependencies
+  apt-get update
+  apt-get install -y --no-install-recommends \
+    locales \
+    wget
+
+  # Get fonts
+  apt-get update
+  echo "ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula select true" | debconf-set-selections
+  apt-get install -y ubuntu-restricted-extras
+
+  # Configure default locale
+  echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
+  locale-gen en_US.utf8
+  /usr/sbin/update-locale LANG=en_US.UTF-8
+  export LC_ALL=en_US.UTF-8
+  export LANG=en_US.UTF-8
+
+  wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
+  apt install -y ./google-chrome-stable_current_amd64.deb
+
+  # Get dependencies
+  apt-get update
+  apt-get install -y software-properties-common
+#  add-apt-repository ppa:ubuntugis/ubuntugis-unstable
+#  apt-get update
+  apt-get install -y --no-install-recommends \
+    libpoppler-cpp-dev \
+    libgfortran4 \
+    libopenblas-dev \
+    libstdc++6 \
+    git \
+    libgit2-dev \
+    libpango1.0-dev \
+    libblas3 \
+    libblas-dev \
+    liblapack-dev \
+    liblapack3 \
+    curl \
+    gcc \
+    fort77 \
+    aptitude \
+    g++ \
+    xorg-dev \
+    libreadline-dev \
+    gfortran \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libxml2-dev \
+    libcairo2-dev \
+    libxt-dev \
+    libbz2-dev \
+    liblzma-dev \
+    ca-certificates \
+    gdebi-core \
+    zlib1g-dev \
+    r-cran-rjags \
+    imagemagick \
+    libmagick++-dev \
+    rng-tools \
+    libtool \
+    libgmp-dev \
+    libmpfr-dev \
+    build-essential \
+    libboost-all-dev \
+    libssh2-1-dev \
+    htop \
+    less \
+    r-cran-rjava \
+    bedtools \
+    libx11-dev \
+    mesa-common-dev \
+    libglu1-mesa-dev \
+    libpcre2-dev \
+    libpcre3-dev \
+    libudunits2-dev \
+    libv8-dev \
+    gdal-bin \
+    libgdal-dev \
+    libproj-dev \
+    libfftw3-dev \
+    libgsl-dev \
+    libsodium-dev \
+    cmake
+
+  apt-get install -y `apt-get --assume-no install texlive-full | \
+    awk '/The following additional packages will be installed/{f=1;next} /Suggested packages/{f=0} f' | \
+    tr ' ' '\n' | \
+        grep -vP 'doc$' | \
+        grep -vP 'texlive-lang' | \
+        grep -vP 'latex-cjk' | \
+        tr '\n' ' '`
+
+  apt-get install -y --no-install-recommends \
+    texlive-lang-german
+
+  cd $HOME
+  wget http://www.fftw.org/fftw-3.3.10.tar.gz --no-check-certificate
+  tar xvf fftw-3.3.10.tar.gz
+  cd fftw-3.3.10
+  ./configure
+  make
+  make install
+
+  cd $HOME
+  wget https://github.com/KlugerLab/FIt-SNE/archive/refs/heads/master.zip --no-check-certificate
+  unzip master.zip
+  cd FIt-SNE-master
+  g++ -std=c++11 -O3  src/sptree.cpp src/tsne.cpp src/nbodyfft.cpp  -o /bin/fast_tsne -pthread -lfftw3 -lm -Wno-address-of-packed-member
+
+  NPROCS=$((`grep -E "^processor" /proc/cpuinfo |tail -1 |awk '{print $3}'` + 1))
+  cd $HOME
+  wget https://cran.rstudio.com/src/base/R-4/R-${R_VERSION}.tar.gz --no-check-certificate
+  tar xvf R-${R_VERSION}.tar.gz
+  cd R-${R_VERSION}
+
+  ./configure --enable-R-shlib=yes
+  echo "Will use make with $NPROCS cores."
+  make -j${NPROCS}
+  make install
+  R --version
+
+  wget \
+    --no-verbose \
+    --no-check-certificate \
+    -O rstudio-server.deb \
+    "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-${RSTUDIO_VERSION}-amd64.deb"
+  gdebi -n rstudio-server.deb
+  rm -f rstudio-server.deb
+
+  cd $HOME
+  wget --no-verbose https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION -O "version.txt" && \
+  VERSION=$(cat version.txt)  && \
+  wget --no-verbose "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
+  gdebi -n ss-latest.deb && \
+  rm -f version.txt ss-latest.deb && \
+  . /etc/environment && \
+  chown shiny:shiny /var/lib/shiny-server
+  mkdir -p /var/log/shiny-server
+  chown shiny.shiny /var/log/shiny-server
+
+  # Clean up
+  rm -rf /var/lib/apt/lists/*
+  # Remove shared semaphore workaround for miniconda
+  if [ -f /rm_run_shm ]; then
+        rm /run/shm;
+        rm /rm_run_shm
+  fi

singularity/rsession.conf

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+r-libs-user=~/R/x86_64-pc-linux-gnu-library/4.2.2.RStudioServer
+session-timeout-minutes=0

singularity/rstudio_auth.sh

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+#!/usr/bin/env bash
+
+# Confirm username is supplied
+if [[ $# -lt 1 ]]; then
+  echo "Usage: auth USERNAME"
+  exit 1
+fi
+USERNAME="${1}"
+
+# Confirm password environment variable exists
+if [[ -z "${RSTUDIO_PASSWORD}" ]]; then
+  echo "The environment variable RSTUDIO_PASSWORD is not set"
+  exit 1
+fi
+
+# Read in the password from user
+read -s -p "Password: " PASSWORD
+echo ""
+
+# Authenticate user
+if [[ "${USER}" == "${USERNAME}" && "${PASSWORD}" == "${RSTUDIO_PASSWORD}" ]]; then
+  echo "Successful authentication"
+  exit 0
+else
+  echo "Invalid authentication"
+  exit 1
+fi

singularity/run.sh

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+#!/bin/sh
+
+module load Singularity
+# or install singularity: https://docs.sylabs.io/guides/latest/user-guide/quick_start.html
+
+# You can remove the following line if there is nothing to bind
+export SINGULARITY_BINDPATH="/mnt/metadata/,/mnt/workdata/"
+
+# Define your port
+export RSTUDIO_PORT=8072
+
+# we don't want to clutter the cluster directories, so each user sets up his own
+# rstudio-server-tmp for now
+export TMPDIR="/homes/olymp/$USER/RStudio-Server-Files/"
+
+echo "Path where RStudio Server will write run-time state, logs, etc.:"
+echo $TMPDIR
+
+mkdir -p "$TMPDIR/tmp/rstudio-server"
+uuidgen > "$TMPDIR/tmp/rstudio-server/secure-cookie-key"
+# the secure cookie should of course only be accessible by the owner
+chmod 0600 "$TMPDIR/tmp/rstudio-server/secure-cookie-key"
+
+mkdir -p "$TMPDIR/var/lib"
+mkdir -p "$TMPDIR/var/run"
+
+RSTUDIO_PASSWORD="password" singularity "$1" \
+  --bind="$TMPDIR/var/lib:/var/lib/rstudio-server" \
+  --bind="$TMPDIR/var/run:/var/run/rstudio-server" \
+  --bind="$TMPDIR/tmp:/tmp" \
+  "$2" \
+  --server-user $USER \
+  --www-port $RSTUDIO_PORT \
+  --auth-none 0 \
+  --auth-pam-helper ~/projects/example/singularity/rstudio_server/rstudio_auth.sh \
+  --rsession-config-file ~/projects/example/singularity/rstudio_server/rsession.conf \
+  --auth-timeout-minutes=0 \
+  --auth-stay-signed-in-days=7