Hi, I was trying to create a custom conda environment. (I was hoping to install packages that don’t seem to be compatible with conda/analysis3.) If I try to run conda init I get the same kind of errors that @mmr0 got in her post: [image] Xp65 conda init fails General …

Hi @dkhutch , On Gadi is preferrable not to run conda init, but rather use an already available conda/micromamba executable and setup (similar to what the conda init command would do). Then add a ~/.condarc file for its configuration. I would strongly suggest switching to micromamba, which is much …

I hope somebody comes along to give a better answer here in a bit, but I’ve had that CondaError: Run 'conda init' before 'conda activate' problem on my local machine, and you can just get around it by activating conda manually > source /path/to/conda/bin/activate > conda activate <my_env_name> Doe…

Thanks Jemma. I tried your suggestion but I got this message: source /g/data/xp65/public/apps/med_conda_scripts/analysis3-25.07.d/bin/activate realpath: invalid option -- '/' Try 'realpath --help' for more information. bash: /launcher_conf.sh: No such file or directory FATAL: configuration disall…

Thanks to @jemmajeffree we have a workaround for getting past the conda init problem. If I run: source /g/data/xp65/public/apps/med_conda/etc/profile.d/conda.sh Then this effectively gets past the conda initstage, and after that I can activate my custom environment: conda activate /g/data/y99/dk…

There were some tutorials in the “old” CLEX CMS wiki, but most of the content is outdated, so I would say the updated tutorial is the one I wrote above :smile:

Thanks for the info Davide! That’s handy to have.

Conda init problems

Technical

jemmajeffree (Jemma Jeffree) 26 August 2025 01:26 6

Huh, thanks

Are there docs/tutorials on this somewhere? (and if so, where? If not, would such a thing be possible?) I didn’t realise it existed.

Otherwise I’ll bookmark this post for future reference.

Using conda or micromamba and how to install it

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Conda init problems

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