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CNVkit installation problem

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!

software error
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updated by constharper • constharper • written by donglei.hu • donglei.hu

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

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written by GenoMax GenoMax 
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
• 0 views • link
written by donglei.hu • donglei.hu

Did you get any error when you installed using conda?

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written by GenoMax GenoMax

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

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written by donglei.hu • donglei.hu

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.

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written by Devon Ryan Devon Ryan

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

• 0 views • link
written by donglei.hu • donglei.hu

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

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written by GenoMax GenoMax

1 answer

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

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written by donglei.hu • donglei.hu

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