Question: Variant calling: Sambama sort command not found
0
gravatar for cseplomarton
6 weeks 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 • 93 views
ADD COMMENTlink modified 5 weeks ago by Martina20 • written 6 weeks 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 6 weeks ago by Pierre Lindenbaum127k

Thanks for the tip! I will check it.

ADD REPLYlink written 5 weeks ago by cseplomarton0
1
gravatar for Martina
5 weeks ago by
Martina20
Martina20 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 5 weeks ago by Martina20

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

ADD REPLYlink written 5 weeks ago by cseplomarton0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1005 users visited in the last hour