Labkey virtual machine setup (merlin, onko-nix)

Documents related to virtual machine setup.

Notes on disk management. Growing file system works by creating new partition. Watchout - the last command is called xfs_growfs.

Notes on installation on virtual machine.

Docker

Setup of docker for labkey on git0.

Post-install tasks (handled by image/compose.yaml):

• link files: Files are linked to /data/labkey/files on docker, separate from home or similar directories
• line externalModules (links from /home/labkey/externalModules on host or override in bin/env.sh, compose.yaml)
• update R packages (moved to image)

  docker exec -it config_labkey-web_1 bash
  #system install should be taken care of by Dockerfile
  #sudo apt-get update
  #sudo apt-get install libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev  libharfbuzz-dev libfribidi-dev libtiff5-dev git
  /usr/local/tomcat>R
  >install.packages('devtools')
  >install.packages('ggtools2')
  
  

Update scripts running on labkey PC

1. Install websocket on labkey docker, not required, analysisModule uses java WebSockets directly:

         docker exec -it config_labkey-web_1 bash
   /usr/local/tomcat>cd
   /home/labkey>mkdir -p software/src
   /home/labkey>cd software/src
   /home/labkey/software/src>git clone https://git0.fmf.uni-lj.si/studen/websocket
   /home/labkey/software/src>sed 's/origin=\".*\"/origin="labkey-vm"/' send.py
   #update origin to labkey-vm
   /home/labkey/software/src>cd
   /home/labkey>mkdir venv
   /home/labkey>sudo apt-get install virtualenv
   /home/labkey>virtualenv venv/socket -p python3
   /home/labkey>. venv/socket/bin/activate
   /home/labkey socket >pip install websockets
   /home/labkey socket >deactivate
   #test
   /home/labkey>~/venv/socket/bin/python ~/software/src/websocket/send.py onko-nix.onko-i.si:TEST:1
   #this probably fails, see steps below
   #copy scripts/runPythonLog.sh or use python directly in analysisModule (TODO!)
   
   

2. Run server on host, ie. labkey-public or onko-nix or whatever:

   • Set IPSERVER to external eth0 or like address.
   • Set IPCLIENT to internal docker network address.
   • Run open_port.sh. If needed, delete obsolete 8765 directives with iptables -D instead of iptables -A or iptables -D. Since labkey_network is set to use range, it is enough to use masks, 172.16.1.0/24, say.
   • Edit websocketServer.py and add labkey-vm to origin (this is why previous test failed)
   • Start, websocket/serviceScripts/start.sh
   • Do the suggested monitoring, websocket, also previous point

3. Update server on work pc, rubens, vangogh, etc.:

   • Stop server, websocket/serviceScripts/stop.sh
   • No changes to iptables are needed, since IP address will be the same as for docker host
   • Edit websocketServer.py and add labkey-vm to origin (this is why previous test failed)
   • Start server, websocket/serviceScripts/start.sh
   • Do the suggested monitoring, websocket, including labkey-public to vangogh and docker to vangogh,

   /home/labkey>~/venv/socket/bin/python ~/software/src/websocket/send.py vangogh.fmf.uni-lj.si:TEST:1