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bedapub / besca

BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis
https://bedapub.github.io/besca/
GNU General Public License v3.0
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env yaml file #298

Open schmucr1 opened 1 year ago

schmucr1 commented 1 year ago

Dear @kohleman

Regarding the environment.yml file, would it be possible to add git as requirement as it is used to pull the beda code. And, is the environment name necessary in the yaml file, or would it be better to remove it?

I am building a Docker image by pulling a copy of the environment.yml file, but as git is not in my base image (sure, I may add it) and as my conda env is called "base" and not "besca_dev" it may lead to conflicts.

What you do think?

Thanks and best regards, R.

kohleman commented 1 year ago

Hi @schmucr1, It think you could add git in the environment file. I have no strong opinion, which way is cleaner. The env name base is rather generic and if I install it, I would never remember to which program it would belong to. Therefor I would prefer something with besca in the name. Then it's clear. Maybe you could use sed to replace the string besca_dev with base before using the environment file. Or, do you think that's to much of a hack?

schmucr1 commented 1 year ago

Dear @kohleman

I agree, the "env name" is not problematic. We can leave it as it is now.

Another thing, regarding the packages installed by "pip": is there a specific reason that we use "pip" there, because the packages are in bioconda and source-forge?

Thanks, R.