Running and setting up MhcVizPipe - CaronLab/MhcVizPipe GitHub Wiki

Running MhcVizPipe for the first time

These instructions assume you have installed MhcVizPipe through pip. If you installed the standalone version, you cannot start MhcVizPipe using the instructions under Starting MhcVizPipe below. The descriptions of the settings are valid for both installations, though the paths to NetMHCpan, NetMHCIIpan and GibbsCLuster should not be changed in the standalone version.

Starting MhcVizPipe

  1. From the terminal type in the following and hit enter:

    python3 -m MhcVizPipe.gui

  2. A welcome message should pop up. Somewhere in that message, you will find a web-link. Open it up! (note, you probably will have to right-click it to open it, or you can copy-paste it into your web browser).

  1. 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 (see below).

Checking the default settings

  1. Before you try to run anything, you should check MVP's settings. To do so, click the "Settings" button in the upper-right corner of the screen.

    settings

    This will open up a dialog to edit the settings:

    settings

  2. If you are using the portable version of MhcVizPipe, or if you copied NetMHCpan, NetMHCIIpan and GibbsCluster to a location in your PATH (e.g. /usr/local/bin), you should not need to change anything. It will already be set up to run. In this case, you can skip down to Overview of Settings to see what they all mean and when you might want to change some of them.

    However, if you did not do these things you will need to tell MhcVizPipe exactly how to run NetMHCpan, NetMHCIIpan and GibbsCluster. Go on to step 3.

  3. The things you need to worry about right now are in the [DIRECTORIES] section.

    • What you need to do is point each variable toward something that will start the respective software. If the tools are in your PATH (e.g. you placed them in a bin folder during installation or you used the easy installation script), you can leave the defaults because they will start up the respective programs if they are in the PATH. If they aren't, then you need to point them at the script files you edited in the installing third-party software section.

    • To set the location for each tool, you need to change the text on the right side of the equals signs (i.e. =). For example, to set the variable to find the examples from the installing third-party software section:

      netmhcpan path = /Users/isasirois/Downloads/netMHCpan-4.0/netMHCpan
netmhciipan path = /Users/isasirois/Downloads/netMHCIIpan-4.0/netMHCIIpan
gibbscluster path = /Users/isasirois/Downloads/GibbsCluster-2.0/gibbscluster

    IMPORTANT

    • Do not ever change the section headers (the things in brackets) or anything to the left of an equals sign. If you do, things will not run correctly.

    • Note that nothing gets applied until you click "Done", so you can always click "Cancel" if you want to revert any changes you have made.

    • If you need to go back to the default settings, you can do so by clicking "Load Defaults". Note that the defaults will not be applied until you click "Done", so if you do it by accident you can just click "Cancel"

Overview of Setttings

[DIRECTORIES] - Under this section are the paths to the files which start NetMHCpan, NetMHCIIpan and GibbsCluster, as well as the path to a directory where MhcVizPipe stores temporary and intermediate files. If you have added the above tools to your path as described in the installing third-party software section then you shouldn't need to change the default paths. If the tools are not in your PATH, then see step 3 above.

  • temp directory - Where MhcVizPipe stores temporary and intermediate files. If you don't care, then the default of /tmp/mhcvizpipe is fine. Note that /tmp gets cleared out by your system every so often (e.g. when the computer restarts).
  • netmhcpan version - The version of NetMHCpan you have installed. This is important because the input alleles and output files are formatted slightly differently. You must use one of 4.0 or 4.1.

[ANALYSIS] - Under this section you will find settings related to the creation of sequence motif logos and how MVP utilizes your systems CPUs during analysis.

  • motifs - Whether to make Shannon or Kullback-Liebler logos. Must be one of "kullback-leibler" or "shannon"
  • hobohm - Tells PlotlyLogo whether to perform clustering on the sequence alignments (i.e. sequence weighting). Clustering is done using the Hobohm 1 algorithm.
  • clustering threshold - The similarity cutoff for Hobohm clustering (0.63 is a commonly used value)
  • weight on prior - The weight on pseudo counts. Set to 0 to turn off pseudo counts.
  • max thread - The maximum threads which MhcVizPipe can run at the same time. This is generally equivalent to how many CPUs it uses. If it is -1, then the value is set to the number of CPUs in your computer.

[SERVER] - You shouldn't usually need to change these settings unless you are setting MVP to run over a local network, or if you have some conflict with a port on your computer and you need to change it.

Go!

Now you can analyze samples with MVP.