wiki:QuickStart

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

   wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Pyrococcus_abyssi/NC_001773.fna
   wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Pyrococcus_abyssi/NC_000868.fna
   cat NC_001773.fna NC_000868.fna > Pyrococcus_abyssi.fna

   wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Pyrococcus_horikoshii/NC_000961.fna
   mv NC_000961.fna Pyrococcus_horikoshii.fna

   wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Pyrococcus_furiosus/NC_003413.fna
   mv NC_003413.fna Pyrococcus_furiosus.fna

   wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Thermococcus_kodakaraensis_KOD1/NC_006624.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 )

cd $LEARN_DIR
$LEARN_DIR/bin/LeARN.pl --path_new_release $LEARN_DIR/data/relTherm1 --input data/Pyrococcus_horikoshii.fna --species "Pyrococcus horikoshii" --log log/relTherm.1.log 
$LEARN_DIR/bin/LeARN.pl --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/LeARN.pl --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/LeARN.pl --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/LeARN_AddUser.pl --login therm --email name@domain.org --privilege 1 --passwd motdepasse

5. Select the latest release as the default web release

$LEARN_DIR/bin/LeARN_SetWebRelease.pl --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 9 years ago Last modified on Oct 2, 2009, 3:42:34 PM