How To Install sra-toolkit on Debian 12
Introduction
In this tutorial we learn how to install sra-toolkit on Debian 12.
What is sra-toolkit
sra-toolkit is:
Tools for reading the SRA archive, generally by converting individual runs into some commonly used format such as fastq.
The textual dumpers “sra-dump” and “vdb-dump” are provided in this release as an aid in visual inspection. It is likely that their actual output formatting will be changed in the near future to a stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON THE OUTPUT FORMAT SEEN IN THIS RELEASE.
Other tools distributed in this package are: abi-dump, abi-load align-info bam-load cache-mgr cg-load copycat fasterq-dump fastq-dump, fastq-load helicos-load illumina-dump, illumina-load kar kdbmeta latf-load pacbio-load prefetch rcexplain remote-fuser sff-dump, sff-load sra-pileup, sra-sort, sra-stat, srapath srf-load test-sra vdb-config, vdb-copy, vdb-decrypt, vdb-encrypt, vdb-get, vdb-lock, vdb-passwd, vdb-unlock, vdb-validate
The “help” information will be improved in near future releases, and the tool options will become standardized across the set. More documentation will also be provided documentation on the NCBI web site.
Tool options may change in the next release. Version 1 tool options will remain supported wherever possible in order to preserve operation of any existing scripts.
There are three methods to install sra-toolkit on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install sra-toolkit Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install sra-toolkit using apt-get by running the following command:
sudo apt-get -y install sra-toolkit
Install sra-toolkit Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install sra-toolkit using apt by running the following command:
sudo apt -y install sra-toolkit
Install sra-toolkit 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 sra-toolkit using aptitude by running the following command:
sudo aptitude -y install sra-toolkit
How To Uninstall sra-toolkit on Debian 12
To uninstall only the sra-toolkit package we can use the following command:
sudo apt-get remove sra-toolkit
Uninstall sra-toolkit And Its Dependencies
To uninstall sra-toolkit and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove sra-toolkit
Remove sra-toolkit Configurations and Data
To remove sra-toolkit configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge sra-toolkit
Remove sra-toolkit configuration, data, and all of its dependencies
We can use the following command to remove sra-toolkit configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge sra-toolkit
Dependencies
sra-toolkit have the following dependencies:
- libbz2-1.0
- libc6
- libgcc-s1
- libhdf5-103-1
- libmagic1
- libncbi-vdb3
- libncbi-wvdb3
- libre2-9
- libssl3
- libstdc++6
- libxml2
- zlib1g
References
Summary
In this tutorial we learn how to install sra-toolkit package on Debian 12 using different package management tools: apt, apt-get and aptitude.
