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!
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I just copied a bunch of cnvkit files from ~/anaconda3/bin to ~/bin and then it worked.
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What does
which cnvkit.pytell you? Also trycnvkit.py -h.Did you get any error when you installed using
conda?Didn't seem to. Should there be a directory "cnvkit"? I can remove the directory "anaconda3" and re-install it if that's necessary.
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 activateit.Thank you all for your helpful replies. I think I figured out what the problem is and CNVkit is now running well.
You should post the solution in your comment above so it is usable by someone else in future.
Thanks for the tip. It really works.