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kevinkovalchik edited this page Oct 1, 2021 · 28 revisions

Welcome to the MhcVizPipe (MVP) wiki!

This guide will help you install MhcVizPipe (MVP) and use it for the first time.

Note that MVP runs natively on Linux and Mac systems. If you have a Windows computer, you can follow these instructions to install it using the Windows Subsystem for Linux.

There are two ways to install MhcVizPipe:

  1. You can download a portable package which contains Python and all the required dependencies. The only thing you need to do is download GibbsCluster, NetMHCpan and NetMHCIIpan (from DTU Health Tech) and place them in a directory called "tools" inside the MhcVizPipe directory. This option is completely portable, e.g. you could move the program onto a USB stick and use it on any compatible system.
    • Because of system dependencies of the standalone Python distribution we are using, we cannot guarantee the portable package will work on every computer. However, we have tested in Ubuntu 16.04-20.04, LinuxMint 18, several versions of Mac OSX (>= HighSierra) and using the Windows Subsystem for Linux, and generally have had no problems. If you encounter problems, please try option 2 below.
  2. Install MhcVizPipe into an existing Python environment and configure the settings to point to existing installations of GibbsCluster, NetMHCpan and netMHCIIpan.

Option 1 is preferable if you have limited experience with Python or using a console, or if you just prefer a simple one-folder installation.

Option 2 is preferable if you have some experience working with Python environments and installing packages with pip, and you prefer to set things up yourself.

Notes

  • While option 2 should be possible on a Windows 10 system with WSL, we have not tested this. Windows usage has only been tested using option 1.
  • We have tried to make sure option 1 will work on as many systems as possible. However, some dependencies of the standalone Python builds we use are sometime missing on some systems. If you have problems with the installation that cannot be resolved, then option 2 provides a more sure path to a working installation, albeit without the convenience of a simple double-click to run experience.

Contents

Easy installation

Do-it-yourself installation

  1. Installing Python3 (if needed)
    1. Mac OS installation
    2. Linux installation
  2. Downloading third-party software
  3. Installing third-party software
  4. Installing MhcVizPipe
  5. Setting up MhcVizPipe

Using MhcVizPipe

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