Introduction
In this tutorial we learn how to install pinfish-examples on Kali Linux.
What is pinfish-examples
pinfish-examples is:
The toolchain is composed of the following tools:
-
spliced_bam2gff – a tool for converting sorted BAM
files containing spliced alignments
into GFF2 format. Each read will be represented as a distinct
transcript. This tool comes handy when visualizing spliced
reads at particular loci and to provide input to the rest
of the toolchain. -
cluster_gff – this tool takes a sorted GFF2 file as
input and clusters together reads having similar
exon/intron structure and creates a rough consensus
of the clusters by taking the median of exon
boundaries from all transcripts in the cluster. -
polish_clusters – this tool takes the cluster
definitions generated by cluster_gff and for each
cluster creates an error corrected read by mapping
all reads on the read with the median length
and polishing it using racon. The polished reads
can be mapped to the genome using minimap2 or GMAP. -
collapse_partials – this tool takes GFFs generated
by either cluster_gff or polish_clusters and filters
out transcripts which are likely to be based on RNA
degradation products from the 5’ end. The tool clusters
the input transcripts into “loci” by the 3’ ends and
discards transcripts which have a compatible transcripts
in the loci with more exons.
This package contains a test data set as well as sample scripts
running some test suite provided by Debian also as autopkgtest.
There are three methods to install pinfish-examples 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 pinfish-examples Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install pinfish-examples using apt-get by running the following command:
sudo apt-get -y install pinfish-examplesInstall pinfish-examples Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pinfish-examples using apt by running the following command:
sudo apt -y install pinfish-examplesInstall pinfish-examples 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 pinfish-examples using aptitude by running the following command:
sudo aptitude -y install pinfish-examples
How To Uninstall pinfish-examples on Kali Linux
To uninstall only the pinfish-examples package we can use the following command:
sudo apt-get remove pinfish-examples
Uninstall pinfish-examples And Its Dependencies
To uninstall pinfish-examples and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove pinfish-examples
Remove pinfish-examples Configurations and Data
To remove pinfish-examples configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge pinfish-examples
Remove pinfish-examples configuration, data, and all of its dependencies
We can use the following command to remove pinfish-examples configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pinfish-examples
Dependencies
pinfish-examples have the following dependencies:
References
Summary
In this tutorial we learn how to install pinfish-examples package on Kali Linux using different package management tools: apt, apt-get and aptitude.
