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Tag: environment

Safety and Clobber errors during clone of anaconda base environment (Version 2022.05)

I installed the anaconda distribution (version 2022.05) on a windows 10 (64 bit) machine. During installation I followed the recommendations given here (installed it only for myself and didn’t add anaconda to the PATH variable). I didn’t change any setting, so you can assume a virgin anaconda with default settings. I need to install some additional packages which aren’t part

Snakemake – How to set conda environment path

In Snakemake, conda environments can be easily set up by defining rules as such conda: “envs/my_environment.yaml”. This way, YAML files specify which packages to install prior to running the pipeline. Some software requires a path to third-party-software, to execute specific commands. An example of this is when generating a reference index with RSEM (example from GitHub page DeweyLab – RSEM):

python conda: created a environment, but it is not using conda’s python

I have been using anaconda for a while, and its Python executable is located at /Users/ufo/opt/anaconda3/bin/python. I have tried to create an environment with conda, and the new environment would use copy this Python to environment’s bin. However, with current Anaconda versation, the new environment will not use anaconda’s Python, but use the original Python pre-installed with Mac OS, which

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