First codebase push. Edited README accordingly.

.gitignore

+# Byte-compiled & optimised
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Eclipse
+.project
+.pydevproject
+.settings
+
+# OSX
+.DS_Store
+
+# Data
+data*
+

README.md

-# Rosetta
-A container-centric Science Platform
+# Rosetta 💁🏽
+
+
+_A container-centric Science Platform_
+
+
+Rosetta makes it easy to run interactive workloads on batch and remote computing systems using Docker and Singularity containers.
+
+
+## Quickstart
+
+Requirements:
+    
+    Bash, Git and Docker. Runs on Linux, Mac or Windows*.
+
+*Windows not supported in development mode due to lack of support for symbolic links.
+
+Setup
+
+	$ rosetta/setup
+
+Build
+
+    $ rosetta/build
+
+Run
+
+	$ rosetta/run
+
+Check status
+
+	$ rosetta/ps
+
+
+### Building errors
+
+It is common for the build process to fail with a "404 not found" error on an apt-get instrucions, as apt repositories often change their IP addresses. In such case, try:
+
+    $ rosetta/build nocache
\ No newline at end of file

Software/MetaDesktop/Dockerfile

+FROM ubuntu:18.04
+MAINTAINER Stefano Alberto Russo <stefano.russo@gmail.com>
+
+#----------------------
+# Basics
+#----------------------
+
+# Set non-interactive
+ENV DEBIAN_FRONTEND noninteractive
+
+# Update first of all
+RUN apt-get update
+
+# Utilities
+RUN apt-get install -y nano telnet unzip wget supervisor build-essential python-dev git-core openjdk-8-jre
+
+
+#------------------------
+# "Meta" user
+#------------------------
+
+# Add group. We chose GID 65527 to try avoiding conflicts.
+RUN groupadd -g 65527 metauser
+
+# Add user. We chose UID 65527 to try avoiding conflicts.
+RUN useradd metauser -d /metauser -u 65527 -g 65527 -m -s /bin/bash
+
+# Add metuaser user to sudoers
+RUN adduser metauser sudo
+
+# Install suodo
+RUN apt-get install sudo -y
+
+# No pass sudo (for everyone, actually)
+COPY files/sudoers /etc/sudoers
+
+#------------------------
+# Supervisor conf
+#------------------------
+
+# Supervisord conf
+COPY files/supervisord.conf /etc/supervisor/
+
+#------------------------
+# VNC
+#------------------------
+
+# Install xvfb that triggers minimal install of X base packages and xterm as sample application
+RUN apt-get install xvfb xterm  -y
+
+# Install base packages for VNC server and headless desktop (2)
+RUN cd /opt && wget https://bintray.com/tigervnc/stable/download_file?file_path=tigervnc-1.8.0.x86_64.tar.gz -O tigervnc-1.8.0.x86_64.tar.gz \
+            && tar -zxvf tigervnc-1.8.0.x86_64.tar.gz \
+            && mv tigervnc-1.8.0.x86_64 tigervnc
+
+# Supervisord configuration
+COPY files/supervisord_vnc.conf /etc/supervisor/conf.d/
+COPY files/run_vnc.sh /etc/supervisor/conf.d/
+RUN chmod 755 /etc/supervisor/conf.d/run_vnc.sh
+
+
+# Web VNC (noVNC) v0.6.1.
+# NOTE: this is a custom version from Doro Wu (fcwu.tw@gmail.com).
+# TODO: Check differences and maybe move to 0.6.2
+COPY files/noVNC.tar.gz /usr/lib/
+RUN cd /usr/lib/ && tar -zxvf noVNC.tar.gz
+COPY files/index.html /usr/lib/noVNC
+
+RUN apt-get install -y net-tools
+
+# Supervisord configuration
+COPY files/supervisord_webvnc.conf /etc/supervisor/conf.d/
+
+# X environment setup/startup
+RUN apt-get install fluxbox -y
+COPY files/xstartup /opt/tigervnc/
+RUN chmod 755 /opt/tigervnc/xstartup
+
+# Prepare for logs
+RUN mkdir /metauser/logs && chown metauser:metauser /metauser/logs
+
+# Rename metauser home folder as a "vanilla" home folder
+RUN mv /metauser /metauser_vanilla
+
+# Add fluxbox customisations
+COPY files/dot_fluxbox /metauser_vanilla/.fluxbox
+RUN chown -R metauser:metauser /metauser_vanilla/.fluxbox
+COPY files/background.jpg /usr/share/images/fluxbox/background.jpg
+
+
+#----------------------
+# Entrypoint
+#----------------------
+
+# Copy entrypoint
+COPY files/entrypoint.sh /
+
+# Give right permissions
+RUN chmod 755 /entrypoint.sh
+
+# Set entrypoint
+ENTRYPOINT ["/entrypoint.sh"]
+
+# Set user (mainly for Singularity)
+USER metauser
+
+# To access: expose 8590/tcp and 5900/tcp

Software/MetaDesktop/build.sh

+#!/bin/bash
+
+if [ ! -f "Docker/Dockerfile" ]; then
+    # TODO: This check is weak: improve me!
+    echo "Please run this script from the project root folder"
+    exit 1
+fi
+
+# Move to the root directory to allow accessing the code in Docker build context
+OR_DIR=$PWD
+cd Docker
+
+# Are we on a Git repo?
+#echo ""
+#git status &> /dev/null
+#if [[ "x$?" == "x0" ]] ; then
+#    CHANGES=$(git status | grep "Changes not staged for commit") 
+#    if [[ "x$CHANGES" == "x" ]] ; then
+#        TAG=$(git rev-parse HEAD | cut -c1-7)
+#        echo "I will tag this container with the Git short hash \"$TAG\" "
+#    else
+#        TAG="latest"
+#        echo "You have uncomitted changes, I will not tag this container with the Git short hash. "
+#    fi
+#else
+#    TAG="latest"
+#fi
+#echo ""
+
+# Use --no-cache in case of build problems (i.e. 404 not found)
+docker build  . -t sarusso/metadesktop
+
+cd $OR_DIR

Software/MetaDesktop/files/dot_fluxbox/apps

+[app] (name=fbrun)
+  [Position]	(WINCENTER)	{0 0}
+  [Layer]	{2}
+[end]

Software/MetaDesktop/files/dot_fluxbox/init

+session.screen0.tabs.usePixmap:	true
+session.screen0.tabs.maxOver:	false
+session.screen0.tabs.intitlebar:	true
+session.screen0.clientMenu.usePixmap:	true
+session.screen0.iconbar.usePixmap:	true
+session.screen0.iconbar.iconTextPadding:	10
+session.screen0.iconbar.iconWidth:	128
+session.screen0.iconbar.alignment:	Relative
+session.screen0.iconbar.mode:	{static groups} (workspace)
+session.screen0.toolbar.visible:	true
+session.screen0.toolbar.height:	0
+session.screen0.toolbar.onhead:	1
+session.screen0.toolbar.widthPercent:	100
+session.screen0.toolbar.alpha:	255
+session.screen0.toolbar.maxOver:	false
+session.screen0.toolbar.autoHide:	false
+session.screen0.toolbar.layer:	Dock
+session.screen0.toolbar.placement:	BottomCenter
+#session.screen0.toolbar.tools:	prevworkspace, workspacename, nextworkspace, clock, prevwindow, nextwindow, iconbar, systemtray
+session.screen0.toolbar.tools: iconbar, systemtray
+session.screen0.menu.alpha:	255
+session.screen0.tab.placement:	TopLeft
+session.screen0.tab.width:	64
+session.screen0.titlebar.left:	Stick 
+session.screen0.titlebar.right:	Minimize Maximize Close 
+session.screen0.window.focus.alpha:	255
+session.screen0.window.unfocus.alpha:	255
+session.screen0.slit.alpha:	255
+session.screen0.slit.maxOver:	false
+session.screen0.slit.placement:	RightBottom
+session.screen0.slit.autoHide:	false
+session.screen0.slit.acceptKdeDockapps:	true
+session.screen0.slit.onhead:	0
+session.screen0.slit.layer:	Dock
+session.screen0.colPlacementDirection:	TopToBottom
+session.screen0.tabFocusModel:	ClickToTabFocus
+session.screen0.autoRaise:	true
+session.screen0.maxDisableMove:	false
+session.screen0.edgeSnapThreshold:	10
+session.screen0.tooltipDelay:	500
+session.screen0.opaqueMove:	true
+session.screen0.windowPlacement:	RowMinOverlapPlacement
+session.screen0.focusNewWindows:	true
+session.screen0.clickRaises:	true
+session.screen0.maxDisableResize:	false
+session.screen0.windowMenu:	/metauser/.fluxbox/windowmenu
+session.screen0.allowRemoteActions:	false
+session.screen0.strftimeFormat:	%d %b, %a %02k:%M:%S
+session.screen0.focusSameHead:	false
+session.screen0.workspacewarping:	true
+session.screen0.fullMaximization:	false
+session.screen0.defaultDeco:	NORMAL
+session.screen0.noFocusWhileTypingDelay:	0
+session.screen0.menuDelay:	200
+session.screen0.workspaceNames:	Workspace 1,Workspace 2,Workspace 3,Workspace 4,
+session.screen0.rowPlacementDirection:	LeftToRight
+session.screen0.focusModel:	ClickFocus
+session.screen0.showwindowposition:	false
+session.screen0.maxIgnoreIncrement:	true
+session.screen0.workspaces:	1
+session.styleOverlay:	/metauser/.fluxbox/overlay
+session.keyFile:	~/.fluxbox/keys
+session.cacheMax:	200
+session.tabsAttachArea:	Window
+session.slitlistFile:	/metauser/.fluxbox/slitlist
+session.forcePseudoTransparency:	false
+session.tabPadding:	0
+session.colorsPerChannel:	4
+session.styleFile:	/usr/share/fluxbox/styles//ubuntu-light
+session.autoRaiseDelay:	250
+session.cacheLife:	5
+session.appsFile:	/metauser/.fluxbox/apps
+session.ignoreBorder:	false
+session.configVersion:	13
+session.doubleClickInterval:	250
+session.menuFile:	~/.fluxbox/menu

Software/MetaDesktop/files/dot_fluxbox/keys

+# click on the desktop to get menus
+OnDesktop Mouse1 :HideMenus
+OnDesktop Mouse2 :WorkspaceMenu
+OnDesktop Mouse3 :RootMenu
+
+# scroll on the desktop to change workspaces
+OnDesktop Mouse4 :PrevWorkspace
+OnDesktop Mouse5 :NextWorkspace
+
+# scroll on the toolbar to change current window
+OnToolbar Mouse4 :PrevWindow {static groups} (iconhidden=no)
+OnToolbar Mouse5 :NextWindow {static groups} (iconhidden=no)
+
+# alt + left/right click to move/resize a window
+OnWindow Mod1 Mouse1 :MacroCmd {Raise} {Focus} {StartMoving}
+OnWindowBorder Move1 :StartMoving
+
+OnWindow Mod1 Mouse3 :MacroCmd {Raise} {Focus} {StartResizing NearestCorner}
+OnLeftGrip Move1 :StartResizing bottomleft
+OnRightGrip Move1 :StartResizing bottomright
+
+# alt + middle click to lower the window
+OnWindow Mod1 Mouse2 :Lower
+
+# control-click a window's titlebar and drag to attach windows
+OnTitlebar Control Mouse1 :StartTabbing
+
+# double click on the titlebar to shade
+OnTitlebar Double Mouse1 :Shade
+
+# left click on the titlebar to move the window
+OnTitlebar Mouse1 :MacroCmd {Raise} {Focus} {ActivateTab}
+OnTitlebar Move1  :StartMoving
+
+# middle click on the titlebar to lower
+OnTitlebar Mouse2 :Lower
+
+# right click on the titlebar for a menu of options
+OnTitlebar Mouse3 :WindowMenu
+
+# alt-tab
+Mod1 Tab :NextWindow {groups} (workspace=[current])
+Mod1 Shift Tab :PrevWindow {groups} (workspace=[current])
+
+# cycle through tabs in the current window
+Mod4 Tab :NextTab
+Mod4 Shift Tab :PrevTab
+
+# go to a specific tab in the current window
+Mod4 1 :Tab 1
+Mod4 2 :Tab 2
+Mod4 3 :Tab 3
+Mod4 4 :Tab 4
+Mod4 5 :Tab 5
+Mod4 6 :Tab 6
+Mod4 7 :Tab 7
+Mod4 8 :Tab 8
+Mod4 9 :Tab 9
+
+# open a terminal
+Mod1 F1 :Exec x-terminal-emulator
+
+# open a dialog to run programs
+Mod1 F2 :Exec fbrun
+
+# volume settings, using common keycodes
+# if these don't work, use xev to find out your real keycodes
+176 :Exec amixer sset Master,0 1+
+174 :Exec amixer sset Master,0 1-
+160 :Exec amixer sset Master,0 toggle
+
+# current window commands
+Mod1 F4 :Close
+Mod1 F5 :Kill
+Mod1 F9 :Minimize
+Mod1 F10 :Maximize
+Mod1 F11 :Fullscreen
+
+# open the window menu
+Mod1 space :WindowMenu
+
+# exit fluxbox
+Control Mod1 Delete :Exit
+
+# change to previous/next workspace
+Control Mod1 Left :PrevWorkspace
+Control Mod1 Right :NextWorkspace
+
+# send the current window to previous/next workspace
+Mod4 Left :SendToPrevWorkspace
+Mod4 Right :SendToNextWorkspace
+
+# send the current window and follow it to previous/next workspace
+Control Mod4 Left :TakeToPrevWorkspace
+Control Mod4 Right :TakeToNextWorkspace
+
+# change to a specific workspace
+Control F1 :Workspace 1
+Control F2 :Workspace 2
+Control F3 :Workspace 3
+Control F4 :Workspace 4
+Control F5 :Workspace 5
+Control F6 :Workspace 6
+Control F7 :Workspace 7
+Control F8 :Workspace 8
+Control F9 :Workspace 9
+Control F10 :Workspace 10
+Control F11 :Workspace 11
+Control F12 :Workspace 12
+
+# send the current window to a specific workspace
+Mod4 F1 :SendToWorkspace 1
+Mod4 F2 :SendToWorkspace 2
+Mod4 F3 :SendToWorkspace 3
+Mod4 F4 :SendToWorkspace 4
+Mod4 F5 :SendToWorkspace 5
+Mod4 F6 :SendToWorkspace 6
+Mod4 F7 :SendToWorkspace 7
+Mod4 F8 :SendToWorkspace 8
+Mod4 F9 :SendToWorkspace 9
+Mod4 F10 :SendToWorkspace 10
+Mod4 F11 :SendToWorkspace 11
+Mod4 F12 :SendToWorkspace 12
+
+# send the current window and change to a specific workspace
+Control Mod4 F1 :TakeToWorkspace 1
+Control Mod4 F2 :TakeToWorkspace 2
+Control Mod4 F3 :TakeToWorkspace 3
+Control Mod4 F4 :TakeToWorkspace 4
+Control Mod4 F5 :TakeToWorkspace 5
+Control Mod4 F6 :TakeToWorkspace 6
+Control Mod4 F7 :TakeToWorkspace 7
+Control Mod4 F8 :TakeToWorkspace 8
+Control Mod4 F9 :TakeToWorkspace 9
+Control Mod4 F10 :TakeToWorkspace 10
+Control Mod4 F11 :TakeToWorkspace 11
+Control Mod4 F12 :TakeToWorkspace 12

Software/MetaDesktop/files/dot_fluxbox/lastwallpaper

+$full $full|/usr/share/images/fluxbox/ubuntu-light.png|style|:0.0

Software/MetaDesktop/files/dot_fluxbox/menu

+[begin] (fluxbox)
+[include] (/etc/X11/fluxbox/fluxbox-menu)
+[end]

Software/MetaDesktop/files/dot_fluxbox/overlay

+! The following line will prevent styles from setting the background.
+! background: none
+background: aspect
+background.pixmap: /usr/share/images/fluxbox/background.jpg

Software/MetaDesktop/files/dot_fluxbox/windowmenu

+[begin]
+  [shade]
+  [stick]
+  [maximize]
+  [iconify]
+  [raise]
+  [lower]
+  [settitledialog]
+  [sendto]
+  [layer]
+  [alpha]
+  [extramenus]
+  [separator]
+  [close]
+[end]

Software/MetaDesktop/files/entrypoint.sh

+#!/bin/bash
+
+# Exit on any error. More complex thing could be done in future
+# (see https://stackoverflow.com/questions/4381618/exit-a-script-on-error)
+set -e
+
+echo ""
+echo "[INFO] Executing entrypoint..."
+
+#---------------------
+#   Setup home
+#---------------------
+
+# First try without sudo (Singularity with --writable-tmpfs), then sudo (Docker)
+echo "[INFO] Setting up home"
+
+# Get immune to -e inside the curly brackets
+{
+  cp -a /metauser_vanilla /metauser &> /dev/null
+  EXIT_CODE=$?
+} || true
+
+# Check if the above failed and we thus have to use sudo
+if [ "$EXIT_CODE" != "0" ]; then
+    #echo "Using sudo"
+    sudo cp -a /metauser_vanilla /metauser
+fi
+
+# Manually set home (mainly for Singularity)
+echo "[INFO] Setting up HOME env var"
+export HOME=/metauser
+cd /metauser
+
+#---------------------
+#   Save env
+#---------------------
+echo "[INFO] Dumping env"
+
+# Save env vars for later usage (e.g. ssh)
+
+env | \
+while read env_var; do
+  if [[ $env_var == HOME\=* ]]; then
+      : # Skip HOME var
+  elif [[ $env_var == PWD\=* ]]; then
+      : # Skip PWD var
+  else
+      echo "export $env_var" >> /tmp/env.sh
+  fi
+done
+
+#---------------------
+#  Entrypoint command
+#---------------------
+
+if [ "$@x" == "x" ]; then
+    DEFAULT_COMMAND="supervisord -c /etc/supervisor/supervisord.conf"
+    echo -n "[INFO] Executing default entrypoint command: "
+    echo $DEFAULT_COMMAND
+    exec $DEFAULT_COMMAND
+else
+    echo -n "[INFO] Executing entrypoint command: "
+    echo $@
+    exec $@
+fi 
+
+

Software/MetaDesktop/files/index.html

+<html>
+<head>
+<script type="text/javascript">
+function redirecter(){
+    window.location = "./vnc.html?autoconnect=true&resize=remote"
+}
+</script>
+</head>
+<body onLoad="redirecter()">
+Access VNC: click <a href="./vnc.html?autoconnect=true&resize=remote">here</a>.
+</body>
+</html>
\ No newline at end of file

Software/MetaDesktop/files/run_vnc.sh

+#!/bin/bash
+
+# Exec TigerVNC server 
+/opt/tigervnc/usr/bin/vncserver :0 -SecurityTypes None -xstartup /opt/tigervnc/xstartup
+
+# Check it is running. If it is not, exit
+while true
+do
+
+    PSOUT=$(ps -ef | grep /opt/tigervnc/usr/bin/Xvnc | grep SecurityTypes) 
+
+    if [[ "x$PSOUT" == "x" ]] ; then
+        exit 1
+    fi
+
+	# Sleep other 10 secs before re-checking
+	sleep 10
+
+done

Software/MetaDesktop/files/sudoers

+#
+# This file MUST be edited with the 'visudo' command as root.
+#
+# Please consider adding local content in /etc/sudoers.d/ instead of
+# directly modifying this file.
+#
+# See the man page for details on how to write a sudoers file.
+#
+Defaults        env_reset
+Defaults        mail_badpass
+Defaults        secure_path="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
+
+# Host alias specification
+
+# User alias specification
+
+# Cmnd alias specification
+
+# User privilege specification
+root    ALL=(ALL:ALL) ALL
+
+# Members of the admin group may gain root privileges
+%admin ALL=(ALL) ALL
+
+# Allow members of group sudo to execute any command
+%sudo   ALL=(ALL:ALL) NOPASSWD:ALL
+
+# See sudoers(5) for more information on "#include" directives:
+
+#includedir /etc/sudoers.d

Software/MetaDesktop/files/supervisord.conf

+; supervisor config file (modified for our own purpose)
+
+[unix_http_server]
+file=/metauser/.supervisor.sock    ; (the path to the socket file)
+chmod=0700                       ; sockef file mode (default 0700)
+
+[supervisord]
+logfile=/metauser/logs/supervisord.log   ; (main log file;default $CWD/supervisord.log)
+pidfile=/metauser/logs/supervisord.pid   ; (supervisord pidfile;default supervisord.pid)
+childlogdir=/metauser/logs              ; ('AUTO' child log dir, default $TEMP)
+nodaemon=true                   ; Mandatory to run Supervisor in foreground and avoid Docker to exit!
+
+; The below section must remain in the config file for RPC
+; (supervisorctl/web interface) to work, additional interfaces may be
+; added by defining them in separate rpcinterface: sections
+[rpcinterface:supervisor]
+supervisor.rpcinterface_factory = supervisor.rpcinterface:make_main_rpcinterface
+
+[supervisorctl]
+serverurl=unix:///metauser/.supervisor.sock ; use a unix:// URL  for a unix socket
+
+; The [include] section can just contain the "files" setting.  This
+; setting can list multiple files (separated by whitespace or
+; newlines).  It can also contain wildcards.  The filenames are
+; interpreted as relative to this file.  Included files *cannot*
+; include files themselves.
+
+[include]
+files = /etc/supervisor/conf.d/*.conf

Software/MetaDesktop/files/supervisord_vnc.conf

+;=======================================
+; VNC service
+;=======================================
+ 
+[program:vnc]
+ 
+; General
+directory     = /
+command       = /etc/supervisor/conf.d/run_vnc.sh
+numprocs      = 1
+autostart     = true
+autorestart   = true
+startsecs     = 10
+stopwaitsecs  = 30
+process_name  = vnc
+ 
+; Standard out / error
+stdout_logfile          = /metauser/logs/%(program_name)s.log
+stdout_logfile_maxbytes = 5MB
+stdout_logfile_backups  = 10
+stderr_logfile          = /metauser/logs/%(program_name)s.log
+stderr_logfile_maxbytes = 5MB
+stderr_logfile_backups  = 10

Software/MetaDesktop/files/supervisord_webvnc.conf

+;=======================================
+; noVNC service
+;=======================================
+ 
+[program:novnc]
+ 
+; General
+directory     = /usr/lib/noVNC/
+command       = /usr/lib/noVNC/utils/launch.sh --listen 8590
+numprocs      = 1
+autostart     = true
+autorestart   = true
+startsecs     = 10
+stopwaitsecs  = 30
+process_name  = novnc
+ 
+; Standard out / error
+stdout_logfile          = /metauser/logs/%(program_name)s.log
+stdout_logfile_maxbytes = 5MB
+stdout_logfile_backups  = 10
+stderr_logfile          = /metauser/logs/%(program_name)s.log
+stderr_logfile_maxbytes = 5MB
+stderr_logfile_backups  = 10