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Obtaining the HIV‐64148 Pipeline

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Sara Wattanasombat edited this page Aug 16, 2024 · 1 revision

Obtain from Docker Hub

  1. After you’ve installed Docker, you can download the HIV-64148 Pipeline from Docker repository running this command in your terminal.

    docker pull minamini/hiv64148:latest

  2. Check the installation with docker run command.

    docker run --rm minamini/hiv64148:latest hiv64148 -h

    You should see help message printed as a result.

  3. The pipeline has been successfully installed.

Build from source

The best way to install the pipeline is to get it from Docker registry, however, in case you wish to customize the pipeline you might want to build it yourself. There are two ways to get the pipeline the first is to download a Zipped version from the web browser and the second is by git clone command which requires a Git installation.

Obtain the source code

Obtain from zip

  1. Go to HIV-64148 GitHub page
  2. Click on “<> Code” button and select " Download ZIP
  3. Extract the content of the zipped file
    • On Windows, right click and select “Extract All…” then follow the prompt, if the option does not exist or the file cannot be opened by the Explorer, you might need to install additional software such as 7-Zip (https://www.7-zip.org/) to access its content.
    • On MacOS, just double click on the zipped file and it’ll be automatically extracted into the same folder as the zipped file.
    • On Linux, you can use the unzip command unzip file.zip -d destination_folder If unzip command was not found, you can install it with apt sudo apt-get install unzip

Obtain with git clone

  1. Check if you have git installed by opening the terminal (or command prompt in Windows) and enter the git -v command. If there is command not found error, you must install Git by following the instructions here.

  2. In your terminal enter the command:

    git clone https://github.com/STTLab/HIV-64148.git

  3. The repository will be automatically downloaded to your current working directory.

Building the container

  1. Open the terminal/command prompt and navigate to HIV-64148 source code directory.

  2. Run the docker build command:

    docker build -t hiv64148:custom -f ./docker/Dockerfile .

  3. Run your container

    docker run --rm hiv64148:custom hiv64148 -h

Warning

Building from source in Windows may not work as expected due to encoding issue which caused by git automatically convert from Linux to Windows encode, render symlink useless, resulted in a File not found error when running the pipeline with hiv64148 command.

The suggested workaround is to build the image on a Linux machine, dump it, transfer, and load it on to Windows. Alternatively, you can directly invoke the script with docker run … python3 /hiv64148/scripts/main.py -h

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