How to install gigi2
on Red Hat Enterprise Linux





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 Red Hat Enterprise Linux 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 is available for Red Hat Enterprise Linux (RHEL) 7, from the 7.6 release onward, from the Extra Packages for Enterprise Linux (EPEL) repository.

It is not yet available in the EPEL 8 repository, and consequently, not yet available for RHEL 8 unless you build the RPM yourself.

The EPEL repository can be added to your system with the following command:

Adding the optional and extras repositories is also recommended:

sudo subscription-manager repos --enable "rhel-*-optional-rpms" --enable "rhel-*-extras-rpms" sudo yum update

Snap can now be installed as follows:

Once installed, the systemd unit that manages the main snap communication socket needs to be enabled:

To enable classic snap support, enter the following to create a symbolic link between /var/lib/snapd/snap and /snap:

Either log out and back in again or restart your system to ensure snap’s paths are updated correctly.

Install gigi2

To install gigi2, simply use the following command:

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