7  Course setup

7.1 Course setup

Once you have connected to the TRUBA server with your own username, you can begin to setup your folder for the course.

Create the necessary folders:

mkdir -p workshop/data
mkdir -p workshop/logs/slurm
mkdir -p workshop/scripts
mkdir -p workshop/resources
mkdir -p workshop/results/KRAKENUNIQ
mkdir -p workshop/results/MALT_DB
mkdir -p workshop/results/MALT

Create links to the files you will use:

# Create links for the FastQ files
ln -s /truba/home/egitim/workshop/data/* workshop/data
# Create links for the bash scripts 
ln -s /truba/home/egitim/workshop/*.sh workshop
# Create links for the R and python scripts 
ln -s /truba/home/egitim/workshop/scripts/* workshop/scripts
# Create links for the necessary resources files
ln -s /truba/home/egitim/workshop/resources/* workshop/resources
# Create links to the KrakenUniq result
ln -s /truba/home/egitim/workshop/results/KRAKENUNIQ/* workshop/results/KRAKENUNIQ
# Create links to the MALT_DB result
ln -s /truba/home/egitim/workshop/results/MALT_DB/* workshop/results/MALT_DB
# Create links to the MALT result
ln -s /truba/home/egitim/workshop/results/MALT/* workshop/results/MALT

Great, you have now created your workshop folder. From now on, you will be working only from within this folder. Please enter this folder now by using this command:

cd workshop

You can now follow the pipeline step by step. Good luck !