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Developing on virtual computers

Once you have created a virtual computer, attached a disk, and accessed the operating system you are ready to start development on Lightsail for Research by taking the following steps:

  1. Cloning the repository to your virtual computer
  2. Creating and activating a conda environment
  3. Setting up pre-commit

Quick tips about virtual computers

  • Copy and paste need to be synced between your local and remote desktop using the clipboard icon in the upper left hand corner.

    Clipboard

    You will also need to right-click to paste on the virtual desktop; Ctrl+v or Cmd+v will not work.

  • If you use a security key as a multifactor authentication method for GitHub, that will not work on a virtual computer. Make sure you have another way to login with multifactor authentication, such as an authenticator app.

Clone the repository

Virtual computers will have Git and GitKraken installed on them. Click Activities on the upper left hand corner of the Ubuntu desktop then click the 9-dot menu to access the applications on the virtual computer.

Activities
Candy box menu

Open GitKraken and login using GitHub.

Clone the repository to the volume you created and attached following the setup instructions for cloning the repository.

Using the Git CLI

If you prefer to use the command line interface, you can locate and open the Terminal using the same steps (Activities followed by the menu).

Create and activate a conda environment

Conda will be installed on virtual computers, but no setup has been performed.

First, add channels with the following command:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

Create an openscpca conda environment using the environment.yml file in the root of the OpenScPCA-analysis repository. Use the following command in Terminal, replacing {your disk's name} (including the curly brackets) with the name of the disk you cloned the repository to:

cd ~/{your disk's name}/OpenScPCA-analysis
conda env create -f environment.yml

Then, activate the environment with the following command:

conda activate openscpca

Set up pre-commit

Now that you've installed pre-commit into the openscpca environment as described above, you can set up pre-commit following the instructions in our documentation.

Start analyzing

You're ready to start developing on your virtual computer!

Based on the settings ShutdownIdlePercent and ShutdownTimePeriod you specified when you originally created the virtual computer, your computer will shut down automatically after a certain period of low CPU activity. To instead manually shut down the computer when you're done with a coding session, click the Stop computer button from the same screen where you accessed the virtual computer.