get_fragment_length.py command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

get_fragment_length.py: command not found

or when using sudo you get the following error message

sudo: get_fragment_length.py: command not found

Solutions to get_fragment_length.py: command not found

How To Fix get_fragment_length.py: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu get_fragment_length.py is provided by pizzly package.

pizzly is:

For the interpretation of the transcriptome (the abundance and sequence of RNA) of tomour cells one is particularly interested in transcripts that cannot be mapped to single genes but that are seen to be fused as parts from two genes. Likely eplanations are chromosomal translocations.

Pizzly can identify novel such peculiarities, building on interpretations on variable splicing by the tool kallisto. Both tools are elements of the bcbio workflow.

To fix this problem, we can install more using the command below.

sudo apt-get -y install pizzly

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install pizzly.

sudo apt -y install pizzly

Or if you have aptitude installed you can use the following command.

sudo aptitude install pizzly

Summary

In this tutorial we learn how to fix get_fragment_length.py command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.