I work on an SGE cluster where some tools are available with conda :
source activate unicycler-0.4.7
I can use conda on my snakemake workflow with yaml, but in this way, I will going to reinstall the environment.
name: unicycler
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- unicycler=0.4.7
Is it possible to activate an existing environment?
Thanks very much for your helps!
Version :
Best regards,
I should add at the beginning of the Snakefile :
shell.executable("/bin/bash")
shell.prefix("source /usr/local/genome/Anaconda3/etc/profile.d/conda.sh; ")
Prefix to be adapted according to your installation.
After that, envs can be load like in interactive session with conda activate unicycler-0.4.7
for example.