How To Install dazzdb on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 624 words
Introduction
In this tutorial we learn how to install dazzdb on Ubuntu.
What is dazzdb
dazzdb is:
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.
There are three methods to install dazzdb on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install dazzdb Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install dazzdb using apt-get by running the following command:
sudo apt-get -y install dazzdb
Install dazzdb Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install dazzdb using apt by running the following command:
sudo apt -y install dazzdb
Install dazzdb 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. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install dazzdb using aptitude by running the following command:
sudo aptitude -y install dazzdb
How To Uninstall dazzdb on Ubuntu
To uninstall only the dazzdb package we can use the following command:
sudo apt-get remove dazzdb
Uninstall dazzdb And Its Dependencies
To uninstall dazzdb and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove dazzdb
Remove dazzdb Configurations and Data
To remove dazzdb configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge dazzdb
Remove dazzdb configuration, data, and all of its dependencies
We can use the following command to remove dazzdb configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge dazzdb
Dependencies
dazzdb have the following dependencies:
References
Summary
In this tutorial we learn how to install dazzdb package on Ubuntu using different package management tools: apt, apt-get and aptitude.