How To Install pinfish on Kali Linux

In this tutorial we learn how to install pinfish on Kali Linux. pinfish is Collection of tools to annotate genomes using long read transcriptomics data

Introduction

In this tutorial we learn how to install pinfish on Kali Linux.

What is pinfish

pinfish is:

The toolchain is composed of the following tools:

  1. 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.

  2. 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.

  3. 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.

  4. 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.

There are three methods to install pinfish 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 Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install pinfish using apt-get by running the following command:

sudo apt-get -y install pinfish

Install pinfish Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install pinfish using apt by running the following command:

sudo apt -y install pinfish

Install pinfish 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 using aptitude by running the following command:

sudo aptitude -y install pinfish

How To Uninstall pinfish on Kali Linux

To uninstall only the pinfish package we can use the following command:

sudo apt-get remove pinfish

Uninstall pinfish And Its Dependencies

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

sudo apt-get -y autoremove pinfish

Remove pinfish Configurations and Data

To remove pinfish configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge pinfish

Remove pinfish configuration, data, and all of its dependencies

We can use the following command to remove pinfish configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge pinfish

Dependencies

pinfish have the following dependencies:

References

Summary

In this tutorial we learn how to install pinfish package on Kali Linux using different package management tools: apt, apt-get and aptitude.