diff --git a/config/slurm/README.md b/config/slurm/README.md index 191c233..b045df6 100644 --- a/config/slurm/README.md +++ b/config/slurm/README.md @@ -10,6 +10,12 @@ module load PDC bioinfo-tools conda apptainer tmux but the equivalent tool `screen` is pre-installed and does not need to be loaded. +> Apptainer (former singularity) will store its cache per +default in your home directory which will quickly run out of +storage space. You can tell it to use your `scratch` instead, a +temporary directory with unlimited space by adding this row +to your `~/.bashrc`: `export APPTAINER_CACHEDIR=$PDC_TMP`. + 2) After cloning the repository, change permissions for the Snakefile: @@ -19,21 +25,19 @@ chmod 755 Snakefile 3) Create the GenErode conda environment or update an earlier version. The latest conda environment contains the Snakemake -executor plugin for slurm: - -``` -conda env create -f environment.yml -n generode -``` - -- If you want to create a conda environment in a different location -than your home directory, you can provide a path to a directory -for the conda environment to be installed in, and run the following -command instead of the command above: +executor plugin for slurm. Since home directories on Dardel +are limited in storage space, you need to create a directory in +your storage project for the conda environment to be installed +in, and run the following command instead of the command above: ``` conda env create -f environment.yml -p /cfs/klemming/projects/supr/sllstore.../generode ``` +> Note that you can save storage space in your storage project +on Dardel by creating a common GenErode conda environment for +several people. + 4) Copy the configuration file `config/slurm/profile/config_plugin_dardel.yaml` to `slurm/config.yaml`. This file specifies Snakemake and apptainer parameters that are used to run the pipeline, as well as compute @@ -60,16 +64,9 @@ resources specified under`default-resources`. - Open a tmux session (alternatively, you can use screen) -- Activate the GenErode conda environment (created or updated -from `environment.yml`): - -``` -conda activate generode -``` - -If you have created the conda environment in a different directory -than your home directory, run the following commands, replacing the -path to the location of the conda environment accordingly: +- Activate the GenErode conda environment with the +following commands, replacing the path to the location of +the conda environment accordingly: ``` export CONDA_ENVS_PATH=/cfs/klemming/home/.../