Variant calling: Sambama sort command not found

Question

[cseplomarton]

Hi everyone!

However, I previosly installed sambamba (https://github.com/biod/sambamba), the terminal can't find sambamba commads. I looked after the problem, but it is still unsolved (if it matters, I try reproduce this tutorial: https://github.com/ekg/alignment-and-variant-calling-tutorial). Can anyone help me with that?

[Pierre Lindenbaum]

the terminal can't find sambamba commads

PATH problem ? https://opensource.com/article/17/6/set-path-linux

[cseplomarton]

Thanks for the tip! I will check it.

Answer 1

[Martina]

Hello, I can highly recommend to use anaconda package manager. https://www.anaconda.com/distribution/ Check the virtual environment managing tutorial, its super easy and cool and practical. https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html

[cseplomarton]

Thank you too! I seen this "anaconda" earlier and it seems very useful.