How To Install bolt-lmm on Debian 11
Introduction
In this tutorial we learn how to install bolt-lmm
on Debian 11.
What is bolt-lmm
bolt-lmm is:
The BOLT-LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations).
The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model. By default, BOLT-LMM assumes a Bayesian mixture-of-normals prior for the random effect attributed to SNPs other than the one being tested. This model generalizes the standard infinitesimal mixed model used by previous mixed model association methods, providing an opportunity for increased power to detect associations while controlling false positives. Additionally, BOLT-LMM applies algorithmic advances to compute mixed model association statistics much faster than eigendecomposition-based methods, both when using the Bayesian mixture model and when specialized to standard mixed model association.
The BOLT-REML algorithm estimates heritability explained by genotyped SNPs and genetic correlations among multiple traits measured on the same set of individuals. BOLT-REML applies variance components analysis to perform these tasks, supporting both multi-component modeling to partition SNP-heritability and multi-trait modeling to estimate correlations. BOLT-REML applies a Monte Carlo algorithm that is much faster than eigendecomposition-based methods for variance components analysis at large sample sizes.
There are three methods to install bolt-lmm
on Debian 11. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install bolt-lmm Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install bolt-lmm
using apt-get
by running the following command:
sudo apt-get -y install bolt-lmm
Install bolt-lmm Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install bolt-lmm
using apt
by running the following command:
sudo apt -y install bolt-lmm
Install bolt-lmm Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude
using the following command.
sudo aptitude update
After updating apt database, We can install bolt-lmm
using aptitude
by running the following command:
sudo aptitude -y install bolt-lmm
How To Uninstall bolt-lmm on Debian 11
To uninstall only the bolt-lmm
package we can use the following command:
sudo apt-get remove bolt-lmm
Uninstall bolt-lmm And Its Dependencies
To uninstall bolt-lmm
and its dependencies that are no longer needed by Debian 11, we can use the command below:
sudo apt-get -y autoremove bolt-lmm
Remove bolt-lmm Configurations and Data
To remove bolt-lmm
configuration and data from Debian 11 we can use the following command:
sudo apt-get -y purge bolt-lmm
Remove bolt-lmm configuration, data, and all of its dependencies
We can use the following command to remove bolt-lmm
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge bolt-lmm
Dependencies
bolt-lmm have the following dependencies:
- libboost-iostreams1.74.0
- libboost-program-options1.74.0
- libc6
- libgcc-s1
- libgomp1
- libnlopt0
- libopenblas0
- libstdc++6
- zlib1g
References
Summary
In this tutorial we learn how to install bolt-lmm
package on Debian 11 using different package management tools: apt
, apt-get
and aptitude
.