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fix conda install #166

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Jul 24, 2024
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fix conda install #166

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14 changes: 4 additions & 10 deletions bih-cluster/docs/best-practice/software-installation-with-conda.md
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Original file line number Diff line number Diff line change
Expand Up @@ -21,12 +21,14 @@ When you logged into the cluster, please make sure that you also executed `srun`
hpc-login-1:~$ srun --mem=5G --pty bash -i
hpc-cpu-123:~$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
hpc-cpu-123:~$ bash Miniconda3-latest-Linux-x86_64.sh -b -f -p $HOME/work/miniconda
hpc-cpu-123:~$ eval "$(/$HOME/work/miniconda/bin/conda shell.bash hook)"
hpc-cpu-123:~$ conda init
hpc-cpu-123:~$ conda config --set auto_activate_base false
```

This will install conda to `$HOME/work/miniconda`.
This path can be changed to your liking.
Please note that the `$HOME` folder has limited space, so be sure to place it in `work`. More about this [here](../storage/home-quota.md).
You can change the path to your liking, but please note that your `$HOME` folder has limited space.
The `work` subfolder however has a bigger quota. More about this [here](../storage/home-quota.md).

To make bioinformatics software available, we have to add the `bioconda` and
some other channels to the conda configuration:
Expand All @@ -37,14 +39,6 @@ hpc-cpu-123:~$ conda config --add channels default
hpc-cpu-123:~$ conda config --add channels conda-forge
```

!!! warning "Important"
By default conda will automatically activate the (base) environment for new shell sessions.
This can significantly delay your login process and should be turned off:

```sh
hpc-cpu-123:~$ conda config --set auto_activate_base false
```

## Installing software with conda
Installing packages with conda is straight forward:

Expand Down