using packages with conda

Question

[raquel]

Hello everyone

I ran

conda create -n scinkd -c conda-forge -c bioconda r-base r-dplyr r-ggplot2 snakemake meryl pigz samtools

conda init bash

conda activate scinkd

But then I wanted to use the package snakemake and ran

snakemake --use-conda   -np -s SCINKD/SCINKD.v2.1.0.FULL.snakefile

And I got the message

bash: snakemake: command not found

I'm following the SCINKD pipeline but they never mention needing to load anything else. What am I missing? After loading packages to conda do I have to manually load the ones I need to use?

Thanks

[ATpoint]

Cannot reproduce. Is this run via some sort of server/HPC/scheduler/something?

[raquel]

Yes, I'm using SSH session

[ATpoint]

Just to be sure: You ssh into a remote server, correct? Die you setup the conda environment on your local machine or the remote? Must be the remote.