How to install gigi2
on openSUSE





GIGI2 is a computer program to impute missing genotypes on pedigrees. The approach handles large pedigrees by using a Markov Chain Monte Carlo-based program to infer inheritance vectors. Our approach has 2 steps: 1. use the program gl_auto from the MORGAN package to infer inference vectors using genotypes from informative framework markers 2. use GIGI to impute missing genotypes.
Note 1: gl_auto and MORGAN are NOT included in this snap, gl_auto should be obtained through its own channels. GIGI2 inputs are outputs from gl_auto.
Note 2: The strict confinement of this app limits where it can write to. To allow it to write in your home directory, you need to attach the home interface to the snap. Likewise if you need to write to external devices mounted in /mnt or /media.
e.g. 'snap connect gigi2:home :home' to be able to write in your /home/user and 'snap connect gigi2:removable-media :removable-media' to write in /mnt/vol_name and /media/vol_name If you need to write to other locations, then you will need to install the snap in devmode, e.g. 'snap install --devmode gigi2' If it was already installed and you need to install in devmode, then I recommend first removing the currently installed version, 'snap remove gigi2'

Details for gigi2

Last updated
25 November 2018

Enable snaps on openSUSE and install gigi2

Snaps are applications packaged with all their dependencies to run on all popular Linux distributions from a single build. They update automatically and roll back gracefully.

Snaps are discoverable and installable from the Snap Store, an app store with an audience of millions.

Enable snapd

Snap can be installed from the command line on openSUSE Leap 42.3, Leap 15 and Tumbleweed.

You need first add the snappy repository from the terminal. Leap 15 users, for example, can do this with the following command:

Swap out openSUSE_Leap_15.0 for either openSUSE_Leap_42.3 or openSUSE_Tumbleweed if you’re using a different version of openSUSE.

With the repository added, import its GPG key:

Finally, upgrade the package cache to include the new snappy repository:

Snap can now be installed with the following:

You then need to either reboot, logout/login or source /etc/profile to have /snap/bin added to PATH. Additionally, enable and start both the snapd and the snapd.apparmor services with the following commands:

sudo systemctl enable snapd sudo systemctl start snapd

Tumbleweed users also need to run the following:

sudo systemctl enable snapd.apparmor sudo systemctl start snapd.apparmor

Install gigi2

To install gigi2, simply use the following command:

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