1. Installing LeARN

2. Fetch the data and copy the fasta files in your $LEARN_DIR directory as defined during the set-up (e.g /www/LeARN/Thermococcaceae)

   cd $LEARN_DIR/data

   cat NC_001773.fna NC_000868.fna > Pyrococcus_abyssi.fna

   mv NC_000961.fna Pyrococcus_horikoshii.fna

   mv NC_003413.fna Pyrococcus_furiosus.fna

   mv NC_006624.fna Thermococcus_kodakaraensis_KOD1.fna

3. Check your configuration

4. Run the pipeline on the 4 genomes (~ 3/4hours depending your hardware )

$LEARN_DIR/bin/ --path_new_release $LEARN_DIR/data/relTherm1 --input data/Pyrococcus_horikoshii.fna --species "Pyrococcus horikoshii" --log log/relTherm.1.log 
$LEARN_DIR/bin/ --path_old_release $LEARN_DIR/data/relTherm1 --path_new_release $LEARN_DIR/data/relTherm2 --input data/Pyrococcus_abyssi.fna --species "Pyrococcus abyssi" --log log/relTherm.2.log 
$LEARN_DIR/bin/ --path_old_release $LEARN_DIR/data/relTherm2 --path_new_release $LEARN_DIR/data/relTherm3 --input data/Pyrococcus_furiosus.fna --species "Pyrococcus furiosus"  --log log/relTherm.3.log
$LEARN_DIR/bin/ --path_old_release $LEARN_DIR/data/relTherm3 --path_new_release $LEARN_DIR/data/relTherm4 --input data/Thermococcus_kodakaraensis_KOD1.fna --species "Thermococcus kodakaraensis KOD1"  --log log/relTherm.4.log

4. Add a new user with editing privilege

$LEARN_DIR/bin/ --login therm --email --privilege 1 --passwd motdepasse

5. Select the latest release as the default web release

$LEARN_DIR/bin/ --root $LEARN_DIR --release_dir data/relTherm4

6. Access the web server (your url depends your local installation)

At that stage you should be able to browse and query the database

7. Edit the database

  • first click on Home/Connexion? to enter your login and password
  • then go to Home/Status? to load a copy of the database in you private workspace
  • after that step you can select either the public database for browsing or select the private one to edit ncRNA and/or families
Last modified 8 years ago Last modified on Oct 2, 2009, 3:42:34 PM