"The REPET package ( Flutre T. et al, 2011 , Quesneville H. et al. 2005 ) integrates bioinformatics programs in order to tackle biological issues at the genomic scale."¹
The currently installed version is available on environment hpc-env/6.4:
If you want to find out more about REPET on the HPC Cluster, you can use the command
module spider REPET
This will show you basic informations e.g. a short description and the currently installed version.
To load the desired version of the module, use the command, e.g.
module load hpc-env 6.4 module load REPET
Always remember: this command is case sensitive!
Setting up REPET for a project
First of all, you need a project name. The project name must have the same name as the input fasta file.
mkdir test_project cd test_project
Of course, you need to load REPET as described above to continue this walkthrough.
Let's assume you want to work with TEannot and TEdenovo. In this case, you need to copy and modify the corresponding config files.
To get an overview about every config file available, type in ls $REPET_PATH/config
In our current case, we will need three files in our project folder:
cp $REPET_PATH/config/TEdenovo.cfg . cp $REPET_PATH/config/TEannot.cfg . cp REPET_PATH/config/setEnv.sh
This three files need some entries regarding your SQL server and regarding your project.
For setEnv.sh, you need to fill out the lines like this:
vim setEnv.sh ------------- export REPET_HOST="db.repetdb.uni-oldenburg.de" export REPET_USER='repetdb' export REPET_PW='_20REPET19!_' export REPET_DB='repetdb' export REPET_PORT='3306' # Your entries could differ, depending on your work group.
# Also, please note that the single quotes must be preferred to double quoutes because otherwise the special characters like ! could get wrongly interpreted by the shell.
As you can see, there is one database for all users. Should you need an own database for your work group (e.g. for privacy reasons), you can request an own SQL database via our SelfService Desk.
In the same manner, you have to adapt the config files:
vim TEdenovo.cfg ------------ [repet_env] repet_version: 2.5 repet_host: repetdb.uni-oldenburg.de repet_user: repetdb repet_pw: _20REPET19!_ repet_db: repetdb repet_port: 3306 repet_job_manager: slurm [project] project_name: test_project project_dir: ~/test_project/TEdenovo
Please note that the main difference between the .cfg files and the setEnv.sh are the double quotes.
To set the needed environment variables, setEnv.sh needs to be sourced:
But to give you a small example on how the syntax works:
TEdenovo.py -P test_project -C TEdenovo.cfg -S 1 -m Map >& step1.txt
This starts the first of eight calculating steps and and creates a project sub folder (in this case sample_folder_db) as well as a log file step1.txt.