Introduction
In this tutorial we learn how to install sra-toolkit on Kali Linux.
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 Kali Linux. 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 updateAfter 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-toolkitInstall sra-toolkit Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux 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 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 Kali Linux
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 Kali Linux, 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 Kali Linux 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:
References
Summary
In this tutorial we learn how to install sra-toolkit package on Kali Linux using different package management tools: apt, apt-get and aptitude.
