NGS PrimerPlex installation in Windows with GUI

Jump to bottom

aakechin edited this page Aug 27, 2020 · 7 revisions

This is a detailed description of the NGS-PrimerPlex installation in Windows for use with GUI. First, you need to install Docker. For windows 10 users, follow the instructions from this page. This description is based on Windows 7 but for Windows 10 installation steps are easier. Docker requires 64-bit Windows version and the virtualization. Additionaly, NGS-PrimerPlex needs at least 8 Gb RAM (for searching for non-target hybridizations of primers). Open https://docs.docker.com/toolbox/toolbox_install_windows/ and reading it carefully make sure that your computer meets all the requirements. Install Docker Toolbox as it is described in the above instruction.

Now you need to download NGS-PrimerPlex from the GitHub server. It would be better, if you could save it to the folder nearest to C:\ (e.g. C:\Users\User_name):

Go to the folder with NGS-PrimerPlex_master.zip and unzip it. To run NGS-PrimerPlex with GUI, you need to install Python. While installation, select options to install pip and to add python to the PATH. Then, run script (by double-click) install_GUI_windows.bat. This should install all prerequisites, including Kivy Python module:

Before running GUI, it is better to pull the docker NGS-PrimerPlex image manually, because the GUI function is unstable and the progress of it cannot be shown. To pull (i.e. to download) the image, run Docker and paste to the Docker command-line (in Windows 7 you need to click right mouse button to paste something into the docker command-line) one of the following commands: `docker pull aakechin/ngs-primerplex:native` for version without human reference genome or `docker pull aakechin/ngs-primerplex:latest` for the version with the reference genome:

docker_pull

After that open command-line (it's not so difficult as you think!). Command-line can be started in the Start menu and wrting cmd in the search field.

cmd_start

Write 'cd NGS-PrimerPlex-master' and press Enter:

cd_NGS_Primerplex

Start Docker (if you haven't done it earlier) and start NGS-PrimerPlex GUI with the `python main.py`:

python_main

You will get many lines of text in the command-line (it the log of starting the GUI) and GUI-window should be opened:

python_main_output NGS-PrimerPlex_GUI

If you get the error "Could not get list of available docker images", see the corresponding issue. Shortly, you can try to restart ot to check that your virtual machine works.