Easy install mhcvizpipe

Easy installation of MhcVizPipe

This will guide you on how to install the standalone distribution of MhcVizPipe.

You must first download NetMHCpan, NetMHCIIpan and GibbsCluster. If you have not yet downloaded these files, go to the third-party downloads section.

• Note: You don't need to do a full installation of NetMHCpan, NetMHCIIpan or GibbsCluster for MhcVizPipe to work. All you need to do is extract them to the correct location as described below. However, it would be a good idea to install them at some point because MhcVizPipe does not show the full output of the tools, and you will want to run the tools yourself for experiments such as mining peptide lists for novel motifs. If you need help doing so, you can follow our installation instructions for the tools.

Installation of MhcVizPipe

1. Download MhcVizPipe from the releases section of this repository Choose the download which is appropriate for your operating system, i.e. either MacOS or Linux. (if you don't see the downloads section, click on Assets under the release)
   
   
   
   

2. Extract the archive to a location of your choosing. This should create a folder called MhcVizpipe

3. Inside the MhcVizPipe folder, you should find a folder called tools in which there will be a few files.
   
   
   
   

   1. Into this tools folder copy the archives for NetMHCpan, NetMHCIIpan and GibbsCluster:
      
      
      
      

4. Now try running MhcVizPipe by double-clicking the MhcVizPipe executable file in the MhcVizPipe folder:
   
   
   
   

   • If you are using a Mac and are unable to open the program by double-clicking because Apple does not recognize it, try right-clicking the file and chosing "open" from the menu. You should then have the option to choose to run the file even though it is unsigned by Apple.

   1. A terminal window should appear and the executable will start to download some required data files for NetMHCpan and NetMHCIIpan:
      
      

      
      
      

   2. If there are any issues with the download, an error message will appear that will tell you how to download the files yourself and where to put them.

   3. Once the downloads are complete, a welcome message should appear. You will find a URL link in the message. To start the MhcVizPipe GUI, right-click the link or copy-paste it into your web browser.
      
      

      
      
      

5. Now you should be seeing MhcVizPipe for the first time:
   
   
   
   

   • If you want, you can bookmark the page that is running MVP. It will be the same address every time you start the program unless you or someone else changes the server parameters in the settings.

You can now continue to learn how to use MhcVizPipe.