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Conda - "best practices" - UPPMAX
Disclaimer: Instructions below assume that
conda
provided by the module system is working. Please, submit a support request if something does not work or you want to know why is not working.Alternatively - follow this tutorial on how to install own conda on Rackham.
The default conda module is not complete setup and will, by default, cache and install in your $HOME folder which is only 32GB and pretty much, not enough for anything. Follow the instructions below to redirect conda cache and environments to your project folder.
Prepare your conda setup.
Shell environment
This, most probably will activate the
(base)
conda environment.(base)
environment conflicts with other tools especially with python!(base)
environment.(base)
activated.conda
is available by runningconda -V
- If it prints the version you might be OKconda env list
. If it works, then you are all setup. Congratulations!mamba
's solver is "baked" intoconda
, somamba
is not available anymore.Tips
module load conda
provides conda with system-wide configuration/sw/apps/conda/latest/rackham_stage/.condarc
that includes local mirrors that are necessary for offline installation on Bianca. Unfortunately, this puts unnecessary load on the conda dependence solving process which leads to unresolved or toooooo slow installations.Try these options when possible.
--override-channels
to you command. Note, not all commands support it.Example for installing https://github.com/harvardinformatics/degenotate
Troubleshooting
~/.bashrc
for conda configuration and remove these lines - if uncertain - copy them in another file, for safety…conda init --reverse
to reverse the damage. This is problematic only on Rackham and Bianca, where this is not the correct way to activate conda.conda env list
.DONE!
Contacts:
tags:
UPPMAX