CNVkit installation problem
1
0
Entering edit mode
22 months ago
donglei.hu ▴ 10

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 • 841 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
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 REPLY
0
Entering edit mode

Did you get any error when you installed using conda?

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Thanks for the tip. It really works.

ADD REPLY
1
Entering edit mode
22 months ago
donglei.hu ▴ 10

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

ADD COMMENT

Login before adding your answer.

Traffic: 1665 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6