Initial commit.

README.md

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+addRStudio
+==========
+
+addRStudio adds `rstudio` server files to an existing singularity image.
+
+Requirements
+============
+
+Requires [dir2singularity](https://github.com/wtsi-hgi/dir2singularity) installed in d2s subdirectory.
+
+Usage
+=====
+
+Use `module load` to select the desired SoftPack module, and run:
+
+```
+addRStudio /path/to/output.sif
+```

addRStudio

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+#!/bin/bash
+
+declare ARBASE="/software/hgi/installs/softpack/addRStudio";
+declare INSTALL_BASE="/software/hgi/installs/softpack/rstudio/.spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/";
+
+declare REXE="$(which R)";
+declare BASE="$(dirname "$REXE")/singularity.sif";
+declare OUTPUT="$1";
+
+help() {
+	declare exit=0;
+
+	if [ -n "${1:-}" ]; then
+		exit=1;
+
+		echo -e "$1\n";
+	fi;
+
+	cat <<HEREDOC
+Usage: $0 /path/to/outout/image.sif
+
+This program adds rstudio to the loaded SoftPack module, saving the new Singularity image in the given output file.
+HEREDOC
+
+	exit $exit;
+}
+
+if [ ! -f "$BASE" ]; then
+	help "No SoftPack module with R loaded.";
+fi;
+
+if [ "$OUTPUT" = "-h" -o "$OUTPUT" = "--help" ]; then
+	help;
+elif [ -z "$OUTPUT" -o -f "$OUTPUT" ]; then
+	help "No output image file specified or file already exists.";
+fi;
+
+declare version="$(R -e "R.version" -s)";
+declare major="$(echo "$version" | grep "^major" | sed -e 's/^[^ ]* *//' -e 's/ *$//')";
+declare minor="$(echo "$version" | grep "^minor" | sed -e 's/^[^ ]* *//' -e 's/ *$//')";
+
+declare R_VERSION="$major.$minor";
+declare R_PATH="r-4.3.1-bfwldrk76z6f52upk47zepliekn7ayqz";
+declare RSERVER_PATH="rstudio-2024.04.0-pvcozy3fjfw5j4ydi7j3gazf47n64w7g";
+
+case "$R_VERSION" in
+"3.6"|"3.6.0"|"3.6.1"|"3.6.2"|"3.6.3")
+	R_PATH="r-3.6.1-lr5l32iscxwjc66xv4vqs55kfyxqnbk7";
+	RSERVER_PATH="rstudio-2024.04.0-v5b3kvtyes7mfzew3dcrl46m25w4peqw";;
+"4.0"|"4.0.1"|"4.0.2"|"4.0.3")
+	R_PATH="r-4.0.3-mtvoxefp3hv7y2cnllkrui3yurc44xt5";
+	RSERVER_PATH="rstudio-2024.04.0-oegivlu2623umrbfwgqslosygk24djua";;
+"4.1.0")
+	R_PATH="r-4.1.0-5gc5uryd3fwthjljfe4clb6kuyn6vlxh";
+	RSERVER_PATH="rstudio-2024.04.0-ybcgmthilhwrjz57p5eeve6jmsuaierl";;
+"4.1"|"4.1.1"|"4.1.2"|"4.1.3")
+	R_PATH="r-4.1.3-faaljkukyjzv3bgqk3zc4kmf37axsk33";
+	RSERVER_PATH="rstudio-2024.04.0-wf7motz63heqioazbrsqqqd2ysoegdzk";;
+"4.2.2")
+	R_PATH="r-4.2.2-attjfhbgqd6aertwlfis62kmnkqqh3om";
+	RSERVER_PATH="rstudio-2024.04.0-l3zcwq34bdvyfw4ydgwvnzfco5vljiqc";;
+"4.2"|"4.2.3")
+	R_PATH="r-4.2.3-o7l36ehxe6dbsykz4cyei4tzywdxbiph";
+	RSERVER_PATH="rstudio-2024.04.0-do2phksin5s36a2l7x2e7jxs2kpk5r7j";;
+"4.4"|"4.4.0"|"4.4.1")
+	R_PATH="r-4.4.1-zf3d5qbxgbiqsk4ddke3fl6uluwcbqcu";
+	RSERVER_PATH="rstudio-2024.04.0-ordci3t2b3w5yvutqsc5jzzsf5tr7cnh";;
+esac;
+
+"$ARBASE"/d2s/dir2singularity -b "$BASE" -e 'PATH=/opt/rstudio/:$PATH' -o "$OUTPUT" -p "$ARBASE/bin" -p "${INSTALL_BASE}soci-4.0.2-f4igwqxeglkzgll5ldl3lqnildqnyued/" -p "${INSTALL_BASE}sqlite-3.43.2-7egypdqfrrdxkbf2zds4o4rkxnd47wwt/" -p "${INSTALL_BASE}zip-3.0-4cvgf6is23bhmllgfmqnlaun7cnjuqrw/" -p "${INSTALL_BASE}unzip-6.0-cw5vahnjqnhdsxvj3fwzht3f3ccbhmks/" -p "${INSTALL_BASE}gettext-0.22.3-ltq66wekiuczj66vmyva2puj4mbmrjef/" -p "${INSTALL_BASE}readline-8.2-7clojnhdikinks5kstq6uo7bazm6yaqr/" -p "${INSTALL_BASE}libiconv-1.17-kbgjdow6rbsxzdrjfg3eqwjxvpjih5zv/" -p "${INSTALL_BASE}icu4c-67.1-xvrp6h5wp6xbge52dinclmoxdopxor6v/" -p "${INSTALL_BASE}ncurses-6.4-vighowby4kk2yi4qzatqu2jaen5ohtq5/" -p "${INSTALL_BASE}boost-1.83.0-ugpte2erzhszosf7nnv4p2g45cvc24nk/" -p "${INSTALL_BASE}libuuid-1.0.3-fwcptc5lwr35u4iswwuexvk6ahwspemk/" -p "${INSTALL_BASE}linux-pam-1.5.3-uk6tq4vszwtzoizzyuwtgogcv3law333/" -p "${INSTALL_BASE}tclap-1.2.5-z5jfcmmw5nvhlzraxqh4hzl3fhwyj74f/" -p "${INSTALL_BASE}yaml-cpp-0.6.3-sinzpu6oh5qo4msb6rfwjkkiiuqougq3/" -p "${INSTALL_BASE}which-2.21-omcb6tpkncbbe37hsfytbvcnajkadhom/" -p "$INSTALL_BASE$R_PATH" -p "$INSTALL_BASE$RSERVER_PATH" -r "$ARBASE/bin:/opt/rstudio";

bin/rstudio

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+#!/bin/bash
+
+printHelp() {
+	cat <<HEREDOC
+Usage: $0 [OPTIONS]
+
+  Start RStudio server.
+
+Options:
+  --home PATH            home directory inside the container.  [default: $HOME]
+  --pwd PATH             initial working directory inside the container.  [default: $PWD]
+  --r-libs-user PATH     specifies additional directories for R packages. [default: ${R_LIBS_USER:-}]
+  --help
+HEREDOC
+
+	exit "${1:-1}";
+}
+
+declare userPath="$(echo "${R_LIBS_USER:-}" | sed -e 's/:*$//')";
+declare home="$HOME";
+declare RSTUDIO_DEBUG=false;
+declare pwd="$PWD";
+
+checkNotEmpty() {
+	if [ -z "${2:-}" ]; then
+		echo -e "Missing $1 value\n";
+
+		printHelp;
+	fi;
+}
+
+while [ $# -gt 0 ]; do
+	k="$1";
+	shift;
+
+	case "$k" in
+	--home)
+		checkNotEmpty "$k" "${1:-}"
+
+		home="$1";
+		shift;;
+	--pwd)
+		checkNotEmpty "$k" "${1:-}"
+
+		pwd="$1";
+		shift;;
+	--r-libs-user)
+		checkNotEmpty "$k" "${1:-}"
+
+		userPath="$1";
+		shift;;
+	--help)
+		printHelp 0;;
+	--debug)
+		export RSTUDIO_DEBUG=true;;
+	*)
+		echo "Unknown argument: $k";
+
+		printHelp;;
+	esac;
+done;
+
+# RStudio does *not* like the PWD to be too long (not sure on exact limit, but it's significantly less than some lustre paths. 
+declare CONFIG_DIR=~/.rstudio-conf;
+mkdir -p "$CONFIG_DIR"
+
+export MY_PWD="$(mktemp -p "$CONFIG_DIR" -u)";
+
+ln -s "$pwd" "$MY_PWD";
+
+cd "$MY_PWD";
+
+export RSTUDIO_CONF="$(mktemp -p "$CONFIG_DIR" -d)";
+export RSTUDIO_LOG="$RSTUDIO_CONF/log";
+
+cleanup() {
+	cd /;
+
+	# Remove PWD symlink
+	rm -f "$MY_PWD";
+
+	rm -rf "$RSTUDIO_CONF";
+}
+
+if ! $RSTUDIO_DEBUG; then
+	trap cleanup EXIT
+fi;
+
+declare PASSWORD="$(openssl rand -base64 15)";
+
+# Determine free Port
+read LOWERPORT UPPERPORT < /proc/sys/net/ipv4/ip_local_port_range
+declare PORT="";
+while true; do
+	PORT="$(shuf -i $LOWERPORT-$UPPERPORT -n 1)";
+	cat /proc/net/tcp | grep -q ":$(printf "%04X" $PORT) " || break;
+done;
+
+declare RSERVER_CONF="$RSTUDIO_CONF/rserver.conf";
+declare SINGULARITY="$(dirname "$(which R)")/singularity.sif";
+
+cat > "$RSERVER_CONF" <<HEREDOC
+# RStudio Server Configuration File
+www-port=$PORT
+server-user=$USER
+server-pid-file=$RSTUDIO_CONF/pid
+server-data-dir=$RSTUDIO_CONF/data
+auth-none=0
+auth-timeout-minutes=0
+auth-stay-signed-in-days=30
+auth-pam-helper-path=$RSTUDIO_CONF/pam
+database-config-file=$RSTUDIO_CONF/database.conf
+secure-cookie-key-file=$RSTUDIO_CONF/cookie
+rsession-which-r=$(echo /software/hgi/installs/softpack/rstudio/.spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/r-*/bin/R)
+rsession-config-file=$RSTUDIO_CONF/session.conf
+HEREDOC
+
+{
+	cat <<HEREDOC
+session-save-action-default=no
+session-timeout-minutes=0
+session-timeout-suspend=0
+HEREDOC
+
+	declare rlibs="/opt/view/rlib/R";
+
+#	if [ -n "$userPath" ]; then
+#		rlibs="$rlibs:$userPath";
+#	fi;
+
+	export R_LIBS_USER="$rlibs";
+
+	echo -n "r-libs-user=$R_LIBS_USER";
+} > "$RSTUDIO_CONF/session.conf";
+
+cat > "$RSTUDIO_CONF/database.conf" <<HEREDOC
+provider=sqlite
+directory=$RSTUDIO_CONF/database
+HEREDOC
+
+	cat > "$RSTUDIO_CONF/pam" <<HEREDOC
+#!/bin/bash
+
+IFS="" read -rs PASSWORD
+
+[ "$USER" = "\${1}" ] && [ "$PASSWORD" = "\${PASSWORD}" ];
+HEREDOC
+
+if [ ! -f "$home/.config/rstudio/rstudio-prefs.json" ]; then
+	mkdir -p "$home/.config/rstudio/";
+
+	cat > "$home/.config/rstudio/rstudio-prefs.json" <<HEREDOC
+{
+	"save_workspace": "never",
+	"load_workspace": false,
+	"initial_working_directory": "~",
+	"spelling_dictionary_language": "",
+	"posix_terminal_shell": "bash"
+}
+HEREDOC
+fi;
+
+if $RSTUDIO_DEBUG; then
+	echo -e "\nDEBUG OUTPUT: $RSTUDIO_CONF\n\n" | tee -a "$RSTUDIO_LOG";
+
+	echo "HOME: $home";
+	echo "PWD: $PWD";
+	echo "R_VERSION: $R_VERSION";
+	echo;
+
+	echo "$RSERVER_CONF"
+	echo "$RSERVER_CONF" | sed -e 's/./=/g';
+	echo;
+
+	cat $RSERVER_CONF;
+	echo;
+
+	FNAME="$RSTUDIO_CONF/session.conf";
+	echo "$FNAME"
+	echo "$FNAME" | sed -e 's/./=/g';
+	echo;
+
+	cat "$FNAME";
+	echo;
+	echo;
+	FNAME="$RSTUDIO_CONF/database.conf";
+	echo "$FNAME"
+	echo "$FNAME" | sed -e 's/./=/g';
+	echo;
+
+	cat "$FNAME";
+	echo;
+	echo;
+	FNAME="$home/.config/rstudio/rstudio-prefs.json";
+	echo "$FNAME"
+	echo "$FNAME" | sed -e 's/./=/g';
+	echo;
+
+	cat "$FNAME";
+	echo;
+	echo;
+fi;
+
+chmod +x "$RSTUDIO_CONF/pam";
+
+export HOME="$home";
+export LC_ALL="C";
+export LC_COLLATE="C"
+export TZ="UTC";
+export HOSTNAME="$(hostname -A | tr -d ' ')";
+
+{
+	tee -a "$RSTUDIO_LOG" <<HEREDOC
+Point web browser to: http://$HOSTNAME:$PORT
+
+  use username: $USER
+  use password: $PASSWORD
+
+----------
+----------:$(echo "0:$USER:$PASSWORD:$(echo "http://$HOSTNAME:$PORT" | base64 | tr -d '\n'):$(echo "$HOME" | base64 | tr -d '\n')" | base64 | tr -d '\n')
+HEREDOC
+} | grep -v "^----------";
+
+echo $PATH;
+/software/hgi/installs/softpack/rstudio/.spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/rstudio-*/bin/rserver --config-file="$RSERVER_CONF" | tee -a "$RSTUDIO_LOG";