how to invoke two different conda env for the same bash pipeline from bash script

[bala krish]

Hi,

I am developing a pipeline in which i face a issue that i need to use env1 for upstream of pipeline and env2 for downstream of pipeline. So, i created two conda environments (env1 and env2).

Before i start the pipeline, i can start with "source activate env1" and then start my pipeline with ./Pipeline.sh

However, the line inside my script Pipeline.sh "source activate env2" does not activate env2 conda environment for some reason and i need this to be done right after the upstream of pipeline.

Any help to solve this issue is greatly appreciated!

Bala