From f3027f3b121a7ae188dfd617c83e336274d14d70 Mon Sep 17 00:00:00 2001
From: thomas <kreitler@molgen.mpg.de>
Date: Wed, 13 Nov 2024 09:23:34 +0100
Subject: [PATCH] rstudio-server: bug fixes in launcher script, rebuild needed

---
 rstudio-server-2024.09.0-375-1.build.sh | 131 ++++++++++++++++++++++++
 1 file changed, 131 insertions(+)
 create mode 100755 rstudio-server-2024.09.0-375-1.build.sh

diff --git a/rstudio-server-2024.09.0-375-1.build.sh b/rstudio-server-2024.09.0-375-1.build.sh
new file mode 100755
index 0000000..0af210a
--- /dev/null
+++ b/rstudio-server-2024.09.0-375-1.build.sh
@@ -0,0 +1,131 @@
+#! /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