From e190421ba43622191321e52ae36632eac1938801 Mon Sep 17 00:00:00 2001 From: Thomas Date: Wed, 24 Jul 2024 20:05:49 +0200 Subject: [PATCH] fix conda install --- .../software-installation-with-conda.md | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/bih-cluster/docs/best-practice/software-installation-with-conda.md b/bih-cluster/docs/best-practice/software-installation-with-conda.md index 67ba8e9da..273c9c648 100644 --- a/bih-cluster/docs/best-practice/software-installation-with-conda.md +++ b/bih-cluster/docs/best-practice/software-installation-with-conda.md @@ -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 `$HOME` folder has limited space. +The `work` subfolder however has a bigger quota. More about this [here](../storage/home-quota.md). To make bioinformatics software available, we have to add the `bioconda` and some other channels to the conda configuration: @@ -37,14 +39,6 @@ hpc-cpu-123:~$ 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: