rstudio-server-2024.09.0-375-1.build.sh

#! /usr/bin/bash

# COOKIE=$(mcookie|cut -c-8); grep -v V_GREP_ME $0 > /dev/shm/runme-$COOKIE.sh ; sleep 0.3; exec bash /dev/shm/runme-$COOKIE.sh
# TESTING=1

PKG=rstudio-server
VERSION=2024.09.0-375
BUILD=1

CONTAINER_NAME=$PKG-$VERSION-$BUILD-container
CONTAINER_TYPE=sandbox # otherwise a sif is created, but here there is still trouble

PREFIX=/pkg/$PKG-$VERSION-$BUILD
if [ -n "$TESTING" ]; then PREFIX=/scratch/local2/$PKG-$VERSION-$BUILD ; fi

set -xe
umask 022

BUILD_TMPDIR=/scratch/local2/$PKG-$VERSION-$BUILD.$USER.build.tmp
test -d $BUILD_TMPDIR && ( chmod -R u+rwx $BUILD_TMPDIR || true ; rm -rf $BUILD_TMPDIR )
mkdir -p $BUILD_TMPDIR/home
export TMPDIR=$BUILD_TMPDIR
export HOME=$BUILD_TMPDIR/home

mkdir -p $PREFIX
cat >$PREFIX/profile <<-EOF
	PATH=$PREFIX/bin:\$PATH:/usr/local/package/bin
	if [ -d $PREFIX/.compatlibs ]; then export LD_LIBRARY_PATH=$PREFIX/.compatlibs\${LD_LIBRARY_PATH:+:}\$LD_LIBRARY_PATH ; fi
EOF
. $PREFIX/profile

BUILD=$PREFIX/build

mkdir -p $BUILD
cd $BUILD

mkdir -p rstudio-server
cd rstudio-server

# orig: https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.09.0-375-amd64.deb
BEEHIVE=https://beehive.molgen.mpg.de/048f99f73ce9442ef2efca9b92c14a31/rstudio-server-2024.09.0-375-amd64.deb

test -e rstudio-server-$VERSION-amd64.deb || wget -nv $BEEHIVE
test -d rstudio-server || ar p rstudio-server-$VERSION-amd64.deb data.tar.xz | unxz | tar -x --strip-components=3 -f -

cd $BUILD

mkdir -p apptainer
cd apptainer

echo 'root:x:0:0:root:/root:/bin/bash' > passwd
echo 'root:x:0:' > group
echo '# this is just a stub file, needed to keep /usr/sbin/hostconfig happy (almost).' > hostconfig

cat > apptainer.def <<-EOF
	# our build mode
	Bootstrap: scratch

#	%environment
#	  export PATH=''

	# what goes into the container ...
	%files
	  $BUILD/rstudio-server/rstudio-server /apps/rstudio-server
	  $BUILD/apptainer/group      /etc/group
	  $BUILD/apptainer/hostconfig /etc/hostconfig
	  $BUILD/apptainer/passwd     /etc/passwd
	  /etc/services               /etc/services



	# This is a scriptlet that will be executed on the host, not in the container
	%setup
	  ln -s usr/bin  \$APPTAINER_ROOTFS/bin
	  ln -s usr/sbin \$APPTAINER_ROOTFS/sbin
	  ln -s usr/lib  \$APPTAINER_ROOTFS/lib
	  ln -s usr/lib  \$APPTAINER_ROOTFS/lib64

	# %runscript
	#   echo "This is what happens when you run the container..."

	# %post
	#   echo "Hello from inside the container"

EOF

if [ "$CONTAINER_TYPE" = "sandbox" ]; then
  CONTAINER=$CONTAINER_NAME-sandbox
  test -d $CONTAINER && rm -r $CONTAINER
  apptainer build --sandbox $CONTAINER apptainer.def
else
  CONTAINER=$CONTAINER_NAME.sif
  rm -vf $CONTAINER
  apptainer build $CONTAINER apptainer.def
fi

cd $BUILD

mkdir -p launcher
cd launcher

# Need a proper startup for rstudio-server (search: 'rstudio-server docker singularity/apptainer')
# see e.g. https://github.com/oist/BioinfoUgrp/blob/master/RStudio/launch_rserver.sh

GITCOMMIT_PAM_HELPER=a4d695b
GITCOMMIT_LAUNCHER=3f3fc19

wget https://github.molgen.mpg.de/thomas/utilities_for_rstudio_server/raw/$GITCOMMIT_PAM_HELPER/rstudio-server.pam-helper.sh
sed -i \
    -e "/^# @ID@ #/ s,@ID@,source: github.molgen.mpg.de/thomas/utilities_for_rstudio_server rstudio-server.pam-helper.sh $GITCOMMIT_PAM_HELPER," \
    rstudio-server.pam-helper.sh

chmod -c +x rstudio-server.pam-helper.sh

wget https://github.molgen.mpg.de/thomas/utilities_for_rstudio_server/raw/$GITCOMMIT_LAUNCHER/rstudio-server.launcher.sh
sed -i \
  -e "/^# @ID@ #/ s,@ID@,source: github.molgen.mpg.de/thomas/utilities_for_rstudio_server rstudio-server.launcher.sh $GITCOMMIT_LAUNCHER," \
  -e "/^PREFIX=/ s,@PREFIX@,$PREFIX," \
  -e "/^CONTAINER=/ s,@CONTAINER@,$CONTAINER," \
  rstudio-server.launcher.sh

mv rstudio-server.launcher.sh rstudio-server
chmod -c +x rstudio-server

cd $BUILD

# now 'install'
mkdir -vp $PREFIX/bin $PREFIX/libexec
cp -vp launcher/rstudio-server $PREFIX/bin
cp -vp launcher/rstudio-server.pam-helper.sh $PREFIX/bin
mv -v apptainer/$CONTAINER $PREFIX/libexec