update to work with Ubuntu 2204, current cbrain and ruby version

README.md

@@ -1,5 +1,5 @@
 # cbrain-vagrant
-This is a VagrantFile that will provision and create a CBRAIN instance using a base of ubuntu/xenial64.
+This is a VagrantFile that will provision and create a CBRAIN instance using a base of Ubuntu 22.04
 
 The Vagrant provisions an image to provide you with the following components:
 1. An admin account which you will be asked to change the password on upon first instantiation.
@@ -10,9 +10,10 @@ The Vagrant provisions an image to provide you with the following components:
 To use:
 1. vagrant up (will provision)
 1. at the end of the provision process, the temporary CBRAIN password will be displayed in the log
+1. Currently rvm is installed in a direct way. The method of rvm install with rsa key is commented out, it might need several attempts or/and some troubleshooting. You may uncomment it, if you like, on your own risk, but no support is provided
 1. vagrant ssh
 1. cd cbrain/BrainPortal
 1. type 'rails server puma -b 0.0.0.0 -p 3000 -e development'
 1. go to your local browser and type in the address '127.0.0.1:3000' and you should see the CBRAIN login page.
 
-Note the VagrantFile is using the new plugin interface, if would like to change the resources allocated to the Vagrant, you can set the diskspace and memory requirements there, it is currently set to use 8GB of RAM and 20GB of disk space.
+Note the VagrantFile is using the new plugin interface, if would like to change the resources allocated to the Vagrant, you can set the diskspace and memory requirements 

Vagrantfile

@@ -6,7 +6,7 @@
 # backwards compatibility). Please don't change it unless you know what
 # you're doing.
 Vagrant.configure(2) do |config|
-  config.vm.box = "ubuntu/xenial64"
+  config.vm.box = "ubuntu/jammy64"
 
   config.vm.network "forwarded_port", guest: 3000, host: 3000
   # config.vm.network "public_network"
@@ -25,7 +25,7 @@ Vagrant.configure(2) do |config|
       exec "vagrant " + ARGV.join(' ')
   end 
 
-  config.disksize.size="10GB"
+  config.disksize.size="20GB"
 
   config.vm.provider "virtualbox" do |vb|
      vb.memory = "8129"
@@ -53,6 +53,6 @@ Vagrant.configure(2) do |config|
     cd ~/cbrain/BrainPortal
     echo "Please login in to the portal for the first time as user 'admin'"
     cat /tmp/cbinit.txt
-#    rails server thin -e development -p 3000 > ~/cbrain.log &
+#    rails server puma -e development -p 3000 -b 0.0.0.0> ~/cbrain.log &
   SHELL
 end

provision/setup.sh

@@ -4,7 +4,9 @@ logFile=/tmp/provision.log
 
 echo "Installing MySQL Server" > $logFile
 echo "-----------------------------------------------" >> $logFile
-sudo apt-get update
+sudo apt-get update >> $logFile
+sudo apt-get install -y software-properties-common >> $logFile
+
 sudo apt-get install mariadb-server -y >> $logFile
 
 sqlscript="/tmp/tmp.sql"
@@ -20,23 +22,70 @@ echo "FLUSH PRIVILEGES;" >> $sqlscript
 
 cat $sqlscript | sudo mysql -u root >> $logFile
 
+
+echo "Installing Apptainer" > $logFile
+echo "-----------------------------------------------" >> $logFile
+
+
+
+# For the non-setuid installation use these commands:
+
+sudo add-apt-repository -y ppa:apptainer/ppa
+sudo apt-get update >> $logFile
+sudo apt-get install -y apptainer >> $logFile
+
+# For the setuid installation uncomment these:
+# sudo apt install -y apptainer-suid
+
+
 ### Installing Ruby Version Manager
 
 echo "Installing Ruby Version Manager" >> $logFile
 echo "-----------------------------------------------" >> $logFile
 
 cd $HOME
-\curl -sSL https://rvm.io/mpapis.asc | gpg --import - >> $logFile
-\curl -sSL https://get.rvm.io | bash -s stable >> $logFile
 
-source $HOME/.rvm/scripts/rvm >> $logFile
+sudo apt-get install curl libsodium-dev gnupg2 -y >> $logFile
+gpg2 --keyserver hkp://pool.sks-keyservers.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3 7D2BAF1CF37B13E2069D6956105BD0E739499BDB >> $logFile
+
+
+sudo apt-add-repository -y ppa:rael-gc/rvm >> $logFile
+sudo apt-get update >> $logFile
+
+
+sudo apt-get install -y rvm >> $logFile
+
+sudo usermod -a -G rvm $USER >>$logFile
+
+# command curl -ksSL https://rvm.io/mpapis.asc | gpg2 --import - >> $logfile
+# command curl -sSL https://rvm.io/pkuczynski.asc | gpg2 --import - >> $logFile
+# \curl -sSL https://get.rvm.io | bash -s stable >> $logFile
+
+source  /usr/share/rvm/scripts/rvm >> $logFile
 
-echo "Installing Ruby" > $logFile
+echo "Installing Ruby" >> $logFile
 echo "-----------------------------------------------" >> $logFile
+echo "rmv info" >> $logFile
 
 rvm info >> $logFile
-rvm install 2.4 >> $logFile
-rvm --default 2.4 >> $logFile
+
+echo "openssl pkg install" >> $logFile
+
+
+
+echo "export rvm_max_time_flag=20" >> ~/.rvmrc
+rvm fix-permissions system
+rvm fix-permissions user
+
+
+rvm pkg install openssl >> $logFile
+
+
+
+
+rvm install ruby-2.7.2 --with-openssl-dir=/usr/share/rvm/usr  >> $logFile
+
+rvm --default 2.7.2 >> $logFile
 
 ## Get CBRAIN Code
 
@@ -51,9 +100,13 @@ git clone https://github.com/aces/cbrain.git >> $logFile
 echo "Installing additional packages" >> $logFile
 echo "-----------------------------------------------" >> $logFile
 
-sudo apt-get install libmysqlclient-dev -y >> $logFile
+sudo apt-get install libmariadb-dev-compat libmariadb-dev >> $logFile
+#sudo apt-get install libmysqlclient-dev -y >> $logFile
 sudo apt-get install libxml2 libxml2-dev -y >> $logFile
 sudo apt-get install libxslt1.1 -y >> $logFile
+sudo apt-get install libsodium-dev -y >> $logFile
+sudo apt-get install libcurl4-openssl-dev -y >>  $logFile
+
 
 ## create database.yml file
 
@@ -102,26 +155,9 @@ mkdir $HOME/FlatLocalDP
 mkdir $HOME/SshDP
 mkdir $HOME/CBLocalDP
 
-### install docker 
-
-dockerLog=/tmp/docker-install.log
-sudo apt-get install docker.io -y > $dockerLog
-sudo usermod -a -G docker ubuntu >> $dockerLog
-
-## install singularity
-singLog=/tmp/singularity.log
-
-mkdir $HOME/singTemp; cd $HOME/singTemp
-sudo apt-get install python dh-autoreconf build-essential -y > $singLog 
-wget https://github.com/singularityware/singularity/releases/download/2.4.1/singularity-2.4.1.tar.gz >> $singLog
-tar -xvzf singularity-2.4.1.tar.gz >> $singLog
-cd singularity-2.4.1
-./configure --prefix=/usr/local --sysconfdir=/etc >> $singLog
-make >> $singLog
-sudo make install >> $singLog
 
 cd $HOME
-rm -rf $HOME/singTemp
+
 
 #### Set up the BrainPortal Cache and timezone
 cd $HOME/cbrain/BrainPortal
@@ -135,7 +171,7 @@ echo $timezone | xargs -I {} echo 'p=User.first; p.time_zone = "{}"; p.save' | r
 echo $HOME | xargs -I {} echo 'DataProvider.create :id => 2, :name => "LocalDP", :type => "FlatDirLocalDataProvider", :remote_dir => "{}/FlatLocalDP", :description => "Automatically Generated Local Data Provider", :user_id => 1, :group_id => 1, :online => 1' | rails c >> $logFile
 echo $timezone | xargs -I {} echo 'd=DataProvider.where("id=2").first; d.time_zone = "{}"; d.save' | rails c >> $logFile
 
-cat ~/.ssh/id_cbrain_portal.pub >> ~/.ssh/authorized_keys
+cat ~/.ssh/id_cbrain_ed25519.pub >> ~/.ssh/authorized_keys
 echo $HOME | xargs -I {} echo 'DataProvider.create :id => 3, :name => "SshDP", :type => "FlatDirSshDataProvider", :remote_dir => "{}/SshDP", :description => "Automatically Generated SSH Data Provider", :user_id => 1, :group_id => 1, :online => 1' | rails c >> $logFile
 echo $timezone | xargs -I {} echo 'd=DataProvider.where("id=3").first; d.time_zone = "{}"; d.save' | rails c >> $logFile
 echo $USER | xargs -I {} echo 'd=DataProvider.where("id=3").first; d.remote_user = "{}"; d.remote_host = "localhost"; d.remote_port = 22; d.save' | rails c >> $logFile
@@ -148,15 +184,15 @@ echo $timezone | xargs -I {} echo 'd=DataProvider.where("id=4").first; d.time_zo
 
 # Make sure you can see bundle at login
 cd $HOME
-echo 'export PATH="$PATH:$HOME/.rvm/bin"' > .tmpbashrc
-echo  '[[ -s "$HOME/.rvm/scripts/rvm" ]] && source "$HOME/.rvm/scripts/rvm"' >> .tmpbashrc 
+echo 'export PATH="$PATH:/usr/share/rvm/bin"' > .tmpbashrc
+echo  '[[ -s "/usr/share/rvm/scripts/rvm" ]] && source "/usr/share/rvm/scripts/rvm"' >> .tmpbashrc
 cat .bashrc >> .tmpbashrc
 cp .bashrc .bashrc.old
 mv .tmpbashrc .bashrc
 
 # Create the Bourreau
 cd $HOME/cbrain/BrainPortal
 
-echo $HOME | xargs -I {} echo 'RemoteResource.create :id => 2, :name => "LocalBourreau", :type => "Bourreau", :user_id => 1, :group_id => 1, :online => 1, :description => "Automatically Generated Local Bourreau", :ssh_control_host => "localhost", :ssh_control_port => 22, :ssh_control_rails_dir => "{}/cbrain/Bourreau", :tunnel_mysql_port => 3333, :tunnel_actres_port => 3334, :dp_cache_dir => "{}/BorCache", :workers_instances=> 3, :workers_chk_time => 5, :workers_log_to => "combined", :workers_verbose => 1, :read_only => 0, :portal_locked => 0, :cache_trust_expire => 2592000, :cms_class => "ScirUnix", :cms_shared_dir => "{}/BorWork", :docker_executable_name => "docker", :singularity_executable_name => "singularity"' | rails c >> $logFile
+echo $HOME | xargs -I {} echo 'RemoteResource.create :id => 2, :name => "LocalBourreau", :type => "Bourreau", :user_id => 1, :group_id => 1, :online => 1, :description => "Automatically Generated Local Bourreau", :ssh_control_host => "localhost", :ssh_control_port => 22, :ssh_control_rails_dir => "{}/cbrain/Bourreau", :dp_cache_dir => "{}/BorCache", :workers_instances=> 3, :workers_chk_time => 5, :workers_log_to => "combined", :workers_verbose => 1, :read_only => 0, :portal_locked => 0, :cache_trust_expire => 2592000, :cms_class => "ScirUnix", :cms_shared_dir => "{}/BorWork", :docker_executable_name => "docker", :singularity_executable_name => "singularity"' | rails c >> $logFile
 echo $USER | xargs -I {} echo 'p=RemoteResource.where("id=2").first; p.ssh_control_user = "{}"; p.save' | rails c >> $logFile
-echo $timezone | xargs -I {} echo 'p=RemoteResource.where("id=2").first; p.time_zone = "{}"; p.save' | rails c >> $logFile 
+echo $timezone | xargs -I {} echo 'p=RemoteResource.where("id=2").first; p.time_zone = "{}"; p.save' | rails c >> $logFile