How To Install quiva2DB on Kali Linux

One-liner install command

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

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

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

What is quiva2DB and what are the ways to install it?

Before beginning this tutorial, you will need access to a server or computer running Kali Linux. This guide was written specifically with a server running Kali Linux 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 quiva2DB on Kali Linux. 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 quiva2DB 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 quiva2DB using apt by running the following command:

sudo apt -y install dazzdb

Install quiva2DB using apt

Because quiva2DB is available in Kali Linux’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 quiva2DB using apt by running the following command:

sudo apt -y install dazzdb

Install quiva2DB 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 Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating aptitude database, You can install quiva2DB by running the following command:

sudo aptitude -y install dazzdb

How to upgrade (update) a single package quiva2DB 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 quiva2DB, e.g. single package, you should use the following format with the apt-get command/apt command:

sudo apt-get --only-upgrade install dazzdb

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 dazzdb

How To Uninstall quiva2DB from Kali Linux

To uninstall only the quiva2DB package you can execute the following command:

sudo apt-get remove dazzdb

Uninstall quiva2DB and all its dependencies

To uninstall quiva2DB and its dependencies that are no longer needed by Kali Linux, you can use the command below:

sudo apt-get -y autoremove dazzdb

Remove quiva2DB with all configurations and data

To remove quiva2DB configuration and data from your system you can run the following purge command:

sudo apt-get -y purge dazzdb

Remove quiva2DB completely (configurations, data and all of its dependencies)

And lastly, you can run the next command to remove absolutely everything related to quiva2DB package, e.g.: configurations, data and all of its dependencies. Just use this command:

sudo apt-get -y autoremove --purge dazzdb

Extra info and code examples

To facilitate the multiple phases of the dazzler assembler, all the read data is organized into what is effectively a database of the reads and their meta-information. The design goals for this data base are as follows: * The database stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files. This avoids duplicating the same data, once in the source file and once in the database. * The data base can be built up incrementally, that is new sequence data can be added to the data base over time. * The data base flexibly allows one to store any meta-data desired for reads. This is accomplished with the concept of *tracks* that implementors can add as they need them. * The data is held in a compressed form equivalent to the .dexta and .dexqv files of the data extraction module. Both the .fasta and .quiva information for each read is held in the data base and can be recreated from it. The .quiva information can be added separately and later on if desired. * To facilitate job parallel, cluster operation of the phases of the assembler, the database has a concept of a *current partitioning* in which all the reads that are over a given length and optionally unique to a well, are divided up into *blocks* containing roughly a given number of bases, except possibly the last block which may have a short count. Often programs can be run on blocks or pairs of blocks and each such job is reasonably well balanced as the blocks are all the same size. One must be careful about changing the partition during an assembly as doing so can void the structural validity of any interim block-based results.

Conclusion

You now have a full guide on how to install quiva2DB using apt, apt-get and aptitude tools. Also, we showed how to update as a single package and different ways to uninstall the quiva2DB from Kali Linux.

See also: