How To Install baseCalling_Matrix_merger on Ubuntu 21.04

One-liner install command

For those in a hurry, here's a one-line installation command:

sudo apt-get update && sudo apt -y install pirs

But if you are interested in the detailed steps with descriptions, the following information is for you.

What is baseCalling_Matrix_merger and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Ubuntu 21.04. This guide was written specifically with a server running Ubuntu 21.04 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 Ubuntu 21.04. 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 using apt-get

First, update apt database with apt-get using the following command.

sudo apt-get update

After updating apt-get database, You can install baseCalling_Matrix_merger using apt by running the following command:

sudo apt -y install pirs

Install baseCalling_Matrix_merger using apt

Because baseCalling_Matrix_merger is available in Ubuntu 21.04’s default repositories, it is possible to install it from these repositories using the apt packaging system.

To begin, update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install pirs

Install baseCalling_Matrix_merger 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 Ubuntu 21.04. Update apt database with aptitude using the following command.

sudo aptitude update

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

sudo aptitude -y install pirs

How to upgrade (update) a single package baseCalling_Matrix_merger using apt-get?

First, you will need to update packages index. Run update command as usual:

sudo apt-get update

Next, to upgrade only the baseCalling_Matrix_merger, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install pirs

Note that this command will not install any new packages! If you wish to install the package if it doesn't exist you may leave out --only-upgrade part.

sudo apt-get install pirs

How To Uninstall baseCalling_Matrix_merger from Ubuntu 21.04

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

sudo apt-get remove pirs

Uninstall baseCalling_Matrix_merger and all its dependencies

To uninstall baseCalling_Matrix_merger and its dependencies that are no longer needed by Ubuntu 21.04, you can use the command below:

sudo apt-get -y autoremove pirs

Remove baseCalling_Matrix_merger with all configurations and data

To remove baseCalling_Matrix_merger configuration and data from your system you can run the following purge command:

sudo apt-get -y purge pirs

Remove baseCalling_Matrix_merger completely (configurations, data and all of its dependencies)

And lastly, you can run the next command to remove absolutely everything related to baseCalling_Matrix_merger package, e.g.: configurations, data and all of its dependencies. Just use this command:

sudo apt-get -y autoremove --purge 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 apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the baseCalling_Matrix_merger from Ubuntu 21.04.

See also: