Difference between revisions of "REPET 2016"
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Always remember: this command is case sensitive! | 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 need to work with TEannot and TEdenovo. In this case, you need the corresponding config files. | |||
To get an overview about every config file available, type in ''ls $REPET_PATH/config'' | |||
But 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 every line like this: | |||
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. | |||
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 [https://servicedesk.uni-oldenburg.de/tas/public/ SelfService Desk]. | |||
In the same manner, you have to adapt the config files: | |||
[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 | |||
== Documentation == | == Documentation == | ||
You can read [https://biosphere.france-bioinformatique.fr/wikia2/index.php/REPET_practical_course_urgi here] how to start working with REPET. | You can read [https://biosphere.france-bioinformatique.fr/wikia2/index.php/REPET_practical_course_urgi here] how to start working with REPET. |
Revision as of 09:27, 27 June 2019
Introduction
"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
Installed version
The currently installed version is available on environment hpc-env/6.4:
REPET/2.5-foss-2017b-Python-2.7.14
Using REPET
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 need to work with TEannot and TEdenovo. In this case, you need the corresponding config files. To get an overview about every config file available, type in ls $REPET_PATH/config But 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 every line like this:
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.
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:
[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
Documentation
You can read here how to start working with REPET.