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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Docker image of cnvkit does not contain additional scripts #841

Closed MatteoSchiavinato closed 2 months ago

MatteoSchiavinato commented 10 months ago

Hi,

I am an enthusiastic user of your tool. I use it via docker, but since you're managing the docker hub as well, I am opening the issue here because I don't know how to do it from docker hub.

Today I wanted to use the cnv_annotate.py script to add annotation to an analysis I have previously run, and realised that the docker image ( https://hub.docker.com/r/etal/cnvkit/ ) does not contain the additional scripts.

Could you point me at the directory where scripts are, in case they're included? If not, could you please add them to a new container commit?

Thank you!

171909771 commented 10 months ago

I am encountering the same problem.

171909771 commented 10 months ago

The version 0.9.10 installed from conda or docker does not have the function additional scripts. It works well to backward the 0.9.9.

etal commented 2 months ago

I see the problem. It's a gap in the Python packaging that also affects Debian packaging and the Docker image installation.

Easy to fix for Docker at least. The extra scripts will be in the upcoming 0.9.11 Docker image.