CSC Cloud — Using CSC Cloud

Deploying Applications on VMs

1. Install Docker CE & run RStudio server in Docker Container

Pre-requisites, a VM like the one create in Creating and Configuring VMs

In this exercise we will run some commands to run RStudio in docker and check the results.

1. Install Docker CE on your VM

    sudo yum install -y yum-utils device-mapper-persistent-data lvm2
    sudo yum-config-manager --add-repo https://download.docker.com/linux/centos/docker-ce.repo
    sudo yum install docker-ce
   

2. Enable and Start Docker CE on your VM

    sudo systemctl enable --now docker
   

3. Test if Docker CE was successfully started on your VM

    sudo docker run hello-world
   

4. Run Rstudio docker container

    sudo docker container run --rm -p 80:8787 -d -v ${PWD}:/home/rstudio -w /home/rstudio dceoy/rstudio-server
   

   Alternative image location: quay.io/lvarin/rstudio-server

5. Access Rstudio server
   • Use http://VM-IP (remember to open the TCP port 80 (HTTP) in the VM using Security Groups).
   • Login in the Rstudio server with user: rstudio, and password: rstudio.
   • You should see a page like this:

   

6. Stop Rstudio server

    sudo docker stop $(sudo docker ps -q)
   

2. Install RStudio Server

Pre-requisites, a VM like the one create in Creating and Configuring VMs

In this exercise we will run some commands to build RStudio and check the results.

1. Update the VM

    sudo yum update
   

2. Download Rstudio rpm installation package

    wget https://download2.rstudio.org/rstudio-server-rhel-1.1.456-x86_64.rpm
   

3. Install rstudio

    sudo yum localinstall rstudio-server-rhel-1.1.456-x86_64.rpm -y
    sudo yum install R -y
    sudo rstudio-server verify-installation
   

4. Add a new user account to your system

    sudo useradd rstudio
    sudo passwd rstudio
   

   • The second command will ask you for a new password. This is the same password you will use to login in Rstudio.

5. Access Rstudio server

   • Use http://VM-IP:8787 (remember to open port 8787 in the VM using Security Groups).
   • Login in the Rstudio server with user: rstudio, and the password you provided in the previous step.

3. Installing software with Conda

Pre-requisites, a VM like the one create in Creating and Configuring VMs

1. Install bzip2 compression tool

    sudo yum update
    sudo yum install bzip2
   

2. Download and install Conda into the VM

    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
    bash Miniconda3-latest-Linux-x86_64.sh
    source .bashrc
   

3. Add the software channels

    conda config --add channels defaults
    conda config --add channels conda-forge
    conda config --add channels bioconda
   

4. Use Conda to install software

    conda install bwa
   

5. Browse the packages available in the Bioconda repository
   • https://bioconda.github.io/recipes.html#recipes

6. Create a new environment

    conda create -n bwa_env bwa
    conda info --envs
    source activate my_env
   

4. Installing MySQL server in an Ubuntu VM

In this exercise we will install a MySQL server. In the HPC world is common to need a database to coordinate the analysis and store the results.

1. Launch a Virtual machine

   • Launch a virtual machine using the most recent Ubuntu image available (Ubuntu 22.04). You may use the same instructions as in Creating and Configuring VMs, but selecting the “Ubuntu” image instead of “Centos”.

2. Install the database

    sudo apt update
    sudo apt install mysql-server mysql-client -y
   

3. Configure MySQL users

    sudo mysql_secure_installation
    sudo mysql -e "CREATE USER 'dbuser'@'%' IDENTIFIED  WITH mysql_native_password BY 'fakePassword12345';"
   

4. Open MySQL to the internet

   • Use a security group to open the port (3306)

   • In /etc/mysql/mysql.conf.d/mysqld.cnf, change the line bind-address = 127.0.0.1 into bind-address = 0.0.0.0. This makes MySQL to listen to any IP and not only the localhost (127.0.0.1). Then restart the MySQL Service.

   • When connecting, MySQL will ask for the password that was created earlier.

    mysql -u dbuser -p -h **virtual-ip**
   

   • Remember to remove the Virtual machine afterwards.

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