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'
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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.
Snap is available for Red Hat Enterprise Linux (RHEL) 8 and RHEL 7, from the 7.6 release onward.
The packages for RHEL 7, RHEL 8, and RHEL 9 are in each distribution’s respective Extra Packages for Enterprise Linux (EPEL) repository. The instructions for adding this repository diverge slightly between RHEL 7, RHEL 8 and RHEL 9, which is why they’re listed separately below.
The EPEL repository can be added to RHEL 9 with the following command:
sudo dnf install https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm
sudo dnf upgrade
The EPEL repository can be added to RHEL 8 with the following command:
sudo dnf install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm
sudo dnf upgrade
The EPEL repository can be added to RHEL 7 with the following command:
sudo rpm -ivh https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
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:
sudo yum install snapd
Once installed, the systemd unit that manages the main snap communication socket needs to be enabled:
sudo systemctl enable --now snapd.socket
To enable classic snap support, enter the following to create a symbolic link between /var/lib/snapd/snap and /snap:
sudo ln -s /var/lib/snapd/snap /snap
Either log out and back in again or restart your system to ensure snap’s paths are updated correctly.
To install gigi2, simply use the following command:
sudo snap install gigi2
Browse and find snaps from the convenience of your desktop using the snap store snap.
Interested to find out more about snaps? Want to publish your own application? Visit snapcraft.io now.