Question: Variant calling: Sambama sort command not found
0
gravatar for cseplomarton
7 months ago by
cseplomarton0 wrote:

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?

snp alignment • 166 views
ADD COMMENTlink modified 7 months ago by Martina30 • written 7 months ago by cseplomarton0
3

the terminal can't find sambamba commads

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

ADD REPLYlink written 7 months ago by Pierre Lindenbaum130k

Thanks for the tip! I will check it.

ADD REPLYlink written 7 months ago by cseplomarton0
1
gravatar for Martina
7 months ago by
Martina30
Martina30 wrote:

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

ADD COMMENTlink written 7 months ago by Martina30

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

ADD REPLYlink written 7 months ago by cseplomarton0
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