CNVkit installation problem

Question

[donglei.hu]

Hi,

I am new to cnvkit so apologize if this issue has been discussed before. I have followed the instruction to install cnvkit using anacoda 3. I have also run configuration with

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Then I ran conda install cnvkit

After this part, I can't test the installation. Is there supposed to be a directory "cnvkit"? I don't see it in my home directory.

Any help is appreciated!

[GenoMax]

What does which cnvkit.py tell you? Also try cnvkit.py -h.

[donglei.hu]

which cnvkit.py
/usr/bin/which: no cnvkit.py in (/netapp/home/dhu/bin:/netopt/ucsf/ihg/bin:/netopt/ucsf/ihg/bin64:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)

cnvkit.py -h
-bash: cnvkit.py: command not found

[GenoMax]

Did you get any error when you installed using conda?

[donglei.hu]

Didn't seem to. Should there be a directory "cnvkit"? I can remove the directory "anaconda3" and re-install it if that's necessary.

[Devon Ryan]

Conda isn't in your PATH in that shell. Make sure your conda installation is in your path. Also, if you installed cnvkit in a separate enviroment, ensure that you conda activate it.

[donglei.hu]

Thank you all for your helpful replies. I think I figured out what the problem is and CNVkit is now running well.

[GenoMax]

You should post the solution in your comment above so it is usable by someone else in future.

[constharper]

Thanks for the tip. It really works.

Answer 1

[donglei.hu]

I just copied a bunch of cnvkit files from ~/anaconda3/bin to ~/bin and then it worked.