2. Configuring NeSI¶
Here we assume you created an NeSI account and you have a project allocation and an project code.
First, we need to configure NeSI in a way that we can run Snakemake on Mahuika (the cluster we are going to use for our analyses). This involves two steps:
As of June 2019 a Snakemake module exists on NeSI that we can simply load with
module load snakemake/5.5.0-gimkl-2018b-Python-3.7.3. Once loaded, the steps below are not needed anymore. They are still displayed here in case you need a particular Snakemake version installed.
2.1. Loading a module¶
A module on the cluster includes a software package into our path so that we are able to make use of the software. To load a module on the command-line, you only need to type:
$ module load Miniconda3/4.4.10
Once executed, the
conda command should be readily available to you.
Snakemake has now been installed as a module. If yopu are ok with the version you can just use
module load snakemake/5.5.0-gimkl-2018b-Python-3.7.3 instead of the above process.
$ conda create -n my-base snakemake>5.5.0 $ conda activate my-base
Conda will create a
.conda folder in your home directory and store environments in
.conda/envs by default.
Install conda channels to be able to search for bioinformatics software:
$ conda config --add channels defaults $ conda config --add channels bioconda $ conda config --add channels conda-forge