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kevin edited this page Feb 3, 2021 · 7 revisions

Installing MhcVizPipe in Windows

It is possible to install and run MhcVizPipe on a Windows 10 computer, but it requires a few extra steps.

This installation procedure was tested on a Windows 10 computer with WSL1 (WSL is the Windows Subsystem for Linux). If you are already using WSL and aren't sure if you are using WSL1 or WSL2, the following link has some useful information on this, as well as how to use a specific version of WSL: https://docs.microsoft.com/en-us/windows/wsl/install-win10

MhcVizPipe should work using both WSL1 and WSL2, but we have only tested using WSL1. The following procedure might require some modification to work with WSL2.

If you have not used WSL before, it is most likely that it is not yet set up on your computer. The following instructions will help you install WSL1.

Enable Windows Subsystem for Linux
  1. Open Turn Windows features on or off
    1. either by directly searching for it in the start menu
    2. or going clicking in the start menu on
      1. Open Settings
      2. Click on Apps
      3. Under Related settings section, click on Programs and Features
      4. On the left pane click Turn Windows features on or off
  2. Check the Windows Subsystem for Linux option
  3. Click OK
  4. Click Restart now
Installing Linux distros using Microsoft Store
  1. Open Microsoft Store app
  2. Search for Ubuntu
  3. Click the Get(or Install) button
  4. Click the Launch button
  5. Create a username for Ubuntu and press Enter
  6. Specify a password for Ubuntu and press Enter
  7. Confirm the password by entering it again and press enter
Download MhcVizPipe
  1. Download the latest Linux version of MhcVizPipe from https://github.com/CaronLab/MhcVizPipe/releases/latest (if you don't see the downloads section, click on Assets under the release)
    1. Be sure to choose the file with "Linux" in the name. The file extension should be .tar.gz
  2. Extract the file to a convenient location (e.g. in your Documents folder, C:, or anywhere you will remember it). This will create a new folder called MhcVizPipe
Download NetMHCpan, NetMHCIIpan and GibbsCluster
  1. Download the files for NetMHCpan, NetMHCIIpan and GibbsCluster by following the instructions in in the third-party software section.
  2. Open the MhcVizPipe folder created above in Download MhcVizPipe. In it you will find a folder called tools.
  3. Extract the downloaded NetMHCpan, NetMHCIIpan and GibbsCluster files into this tools folder. This should create three new folders in the tools folder: netMHCIIpan-4.0, gibbscluster-2.0 and netMHCpan-4.0 or netMHCpan-4.1
Running MhcVizPipe

  1. Open the Ubuntu app either from the Microsoft Store or from the start menu

  2. Within the Ubuntu console navigate to the newly generated folder MhcVizPipe by invoking the following command:

    cd /mnt/XXX

    where XXX stands for the Windows file path starting with the disk and finishing with the folder containing the installation script.

    IMPORTANT!! The XXX path needs to be formatted to only contains forward slashes, and you need to remove the colon after the drive letter. For example, if this is the Windows path to your folder

    C:\Users\Me\Documents\MhcVizPipe

    then you would format the cd command like this:

    cd /mnt/c/Users/Me/Documents/MhcVizPipe

  3. Once you have moved into the MhcVizPipe directory, invoke the following command:

    chmod +x ./MhcVizPipe.sh

  4. Then invoke:

    ./MhcVizPipe.sh

  5. If this is the first time MhcVizPipe has been run, it will download a couple data files required by NetMHCpan and NetMHCIIpan.

UsingMhcVizPipe
  1. After starting MhcVizPipe as above, a welcome message should appear in the console.
  2. To open the MhcVizPipe interface, either open the link provided in the message, or open a web browser of your choice (e.g. Firefox, Chrome, Microsoft Edge, etc.) and navigate to http://localhost:8080/
Accessing the temp folder of MhcVizPipe

These instructions assume the temp folder is in the default location. If desired, You can change the location in the MhcVizPipe settings.

  1. Open the Windows File Explorer
  2. In the path type \\wsl$\Ubuntu\tmp\mhcvizpipe
  3. Press Enter
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