snakemake: Conda activate not working on MacOS

Snakemake version

rm -rf .snakefile
conda create -c conda-forge -c bioconda -n snakemake snakemake --yes
conda activate snakemake
snakemake --version
# 5.3.0
conda --version
# conda 4.8.3

Describe the bug Snakemake is not finding conda on my computer, so that when I run snakemake --use-conda to execute my script, I see

Activating conda environment: /Users/james/Documents/Github/2020-sequential-adaptation/.snakemake/conda/f4707758
/bin/bash: activate: No such file or directory

from there it keeps running but runs into an error (because a package which is defined in the environment isn’t installed in my snakemake environment.

Additional context The only thing non-standard that I can think of is that I’m using zsh rather than bash for my shell. If I try conda activate .snakemake/conda/f4707758 it works and has the packages I want installed, so I know that Snakemake has successfully created this environment, but is struggling to activate it.

About this issue

Original URL
State: open
Created 4 years ago
Comments: 19 (2 by maintainers)

Most upvoted comments

Hello, I have same issue on a Linux cluster: snakemake wants to load a conda environment with the command “source activate”, but this results in “/usr/bin/bash: activate: No such file or directory”. The environment itself as created by snakemake is fine, I can activate it manually and it has the dependencies. Just snakemake doesn’t seem to know about the conda version!? conda 4.8.2 snakemake 5.3.0 (installed inside a conda environment)

Same here on a different system:

Red Hat Enterprise Linux Server release 7.9 (Maipo)
conda 4.7.12 (no mamba)

Running conda install conda in conda env in which snakemake is installed solved the problem.

+11

renatobellotti on Jul 29, 2021

Having the same problem here on Ubuntu 18.04 LTS on an Amazon EC2 instance; tried the conda install conda trick mentioned by @madil7173 but to no avail, and I get the same results as @mscharmann when I try to activate the environment. I’m overall very confused…

Edit: Updating to snakemake 5.26.1 fixed my issue, sorry to have upped the thread for nothing !

BrunoFant on Oct 2, 2020

Running conda install conda in conda env in which snakemake is installed worked for me too.

jonathandmoore on Dec 21, 2021

Hello, I have same issue on a Linux cluster: snakemake wants to load a conda environment with the command “source activate”, but this results in “/usr/bin/bash: activate: No such file or directory”. The environment itself as created by snakemake is fine, I can activate it manually and it has the dependencies. Just snakemake doesn’t seem to know about the conda version!? conda 4.8.2 snakemake 5.3.0 (installed inside a conda environment)

mscharmann on Sep 7, 2020