How To Install baseCalling_Matrix_merger on CentOS 8

One-liner Install Command

If you are only interested in the installation command, here is a quick answer for you:

sudo yum makecache && sudo yum -y install pirs

sudo dnf makecache && sudo dnf -y install pirs

But if you are interested in the details with step-by-step instructions, the following information will be helpful.

What is baseCalling_Matrix_merger and How to Install It?

First things first, you will need access to a server or computer running CentOS 8. This guide was written specifically with a server running CentOS 8 in mind, although it should also work on older, supported versions of the operating system.

Also, make sure you are running a regular, non-root user with sudo privileges configured on your server. When you have an account available, log in as your non-root user to begin.

There are several ways to install baseCalling_Matrix_merger on CentOS 8. You can use (links are clickable):

In the following sections, we will describe each method in detail. You can choose one of them or refer to the recommended one.

Install baseCalling_Matrix_merger on CentOS 8 using dnf

First, update dnf packages database with dnf by running the next command:

sudo dnf makecache --refresh

After updating database, You can install baseCalling_Matrix_merger using dnf by running the following command:

sudo dnf -y install pirs

Install baseCalling_Matrix_merger on CentOS 8 using yum

Because baseCalling_Matrix_merger is available in CentOS 8’s default repositories, it is possible to install it from these repositories using the yum packaging system.

To begin, update local packages database with yum using the following command.

sudo yum makecache --refresh

Now can install baseCalling_Matrix_merger package on your server/computer by running the following command:

sudo yum -y install pirs

How to upgrade (update) a single package baseCalling_Matrix_merger using yum?

To update all the packages available on the system:

yum update

If you want to update a specific package like baseCalling_Matrix_merger in this example you should use the following command:

yum update pirs

To downgrade a package to an earlier version:

yum downgrade pirs

How to Upgrade baseCalling_Matrix_merger on CentOS 8 with dnf?

When you run the dnf update, all system packages with available updates are updated. However, if you want to upgrade a single package, then you would have to pass the package name as the argument to the dnf update command.

dnf update pirs

How To remove baseCalling_Matrix_merger from CentOS 8

To uninstall only the baseCalling_Matrix_merger package you can execute the following command:

sudo dnf remove pirs

Extra info and code examples

The program pIRS can be used for simulating Illumina PE reads, with a series of characters generated by Illumina sequencing platform, such as insert size distribution, sequencing error(substitution, insertion, deletion), quality score and GC content-coverage bias. The insert size follows a normal distribution, so users should set the mean value and standard deviation. Usually the standard deviation is set as 1/20 of the mean value. The normal distribution by Box-Muller method is simulated. The program simulates sequencing error, quality score and GC content- coverage bias according to the empirical distribution profile. Some default profiles counted from lots of real sequencing data are provided. To simulate reads from diploid genome, users should simulate the diploid genome sequence firstly by setting the ratio of heterozygosis SNP, heterozygosis InDel and structure variation.

Conclusion

You now have a full guide on how to install baseCalling_Matrix_merger using dnf and yum package managers. Also, we showed how to update manually as a single package and different ways to uninstall the baseCalling_Matrix_merger from CentOS 8.

See also: