Question: CNVkit installation problem
0
gravatar for donglei.hu
13 months ago by
donglei.hu10
donglei.hu10 wrote:

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 • 531 views
ADD COMMENTlink modified 13 months ago by constharper0 • written 13 months ago by donglei.hu10

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

ADD REPLYlink modified 13 months ago • written 13 months ago by genomax85k
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
ADD REPLYlink modified 13 months ago • written 13 months ago by donglei.hu10

Did you get any error when you installed using conda?

ADD REPLYlink written 13 months ago by genomax85k

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

ADD REPLYlink written 13 months ago by donglei.hu10

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.

ADD REPLYlink written 13 months ago by Devon Ryan95k

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

ADD REPLYlink written 13 months ago by donglei.hu10

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

ADD REPLYlink written 13 months ago by genomax85k

Thanks for the tip. It really works.

ADD REPLYlink written 13 months ago by constharper0
1
gravatar for donglei.hu
13 months ago by
donglei.hu10
donglei.hu10 wrote:

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

ADD COMMENTlink written 13 months ago by donglei.hu10
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