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Human-Augment-Analytics / CichlidBowerTracking

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Cichlid Bower Tracking

Table of Contents

How to Setup Conda Environment

This section explains how to setup the environment used by this repo. If your preferred method isn't listed here, please feel free to add the step-by-step process here.

Windows WSL2 (Ubuntu x86)

  1. Open the WSL2 command line in cmd.exe.
  2. Create a directory for miniconda3 by entering the command mkdir -p ~/miniconda3 1.
  3. Get miniconda.sh from the official server by entering wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh 1.
  4. Enter the command bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3 1.
  5. Delete miniconda.sh by entering the command rm -rf ~/miniconda3/miniconda.sh 1.
  6. Enter the command ~/miniconda3/bin/conda init bash and then close the WSL2 command line tab in cmd.exe 1.
  7. Re-open the WSL2 command line in cmd.exe and open ~/.bashrc in the nano editor by entering the command nano ~/.bashrc 2.
  8. Add export PATH=~/miniconda3/bin:$PATH to the end of the ~/.bashrc file using nano, and save the changes.
  9. Exit the nano editor and run the command source ~/.bashrc to enact the changes made.
  10. Open a Windows Powershell tab in cmd.exe and run the command wsl --shutdown 4.
  11. Reopen the WSL2 commmand line in cmd.exe and enter the command conda --version; if you get a version number as output, miniconda is correctly installed.
  12. Traverse to the desired directory in your file system and clone this repo using git clone https://github.com/charlesrclark1243/CichlidBowerTracking.git.
  13. Setup the environment by entering the command conda env create -f cichlidbowertracking.yml 3.
  14. If you get the error CondaSSLError: Encountered an SSL error. Most likely a certificate verification issue. try running the previous command again and it will likely pickup with the setup exactly where it left off before the error.

How to Setup Rclone Remote

This section explains how to setup the rclone remote used to connect to the Dropbox. If your preferred method isn't listed here, please feel free to add the step-by-step process here.

Windows WSL2 (Ubuntu x86)

  1. Install rclone using the Ubuntu command line, e.g., sudo apt install.
  2. Download the rclone file from BioSci-McGrath/Apps/CichlidPiData/__CredentialFiles/ Dropbox directory.
  3. Move the downloaded rclone file from your Windows Downloads folder to /home/<wsl-user>/.config/rclone/.
  4. Run the command rclone config and rename the rclone remote from cichlidVideo to CichlidPiData.
  5. Reconnect to the rclone remote by running rclone config reconnect CichlidPiData: and following the provided prompts.

References

  1. "Miniconda: Quick command line install," docs.anaconda.com. https://docs.anaconda.com/free/miniconda/#quick-command-line-install.
  2. P. Sawe, "Conda Command Not Found," medium.com. https://medium.com/@sawepeter6/conda-command-not-found-ac28bea24291.
  3. L. Gonzalez, "How to make new anaconda env from yml file," stackoverflow.com. https://stackoverflow.com/a/59686678.
  4. "Miniconda on WSL2 (Ubuntu 20.04) fails with CondaHTTPError: HTTP 000 CONNECTION FAILED," stackoverflow.com. https://stackoverflow.com/questions/67923183/miniconda-on-wsl2-ubuntu-20-04-fails-with-condahttperror-http-000-connection.