This protocol uses the Makefile install-genome-flat-files.mk. This procedure supports the installation of arbitrary genomes from any source, provided that 4 input files are obtained with the following extensions:

  • $SPECIES_RSAT_ID.dna.toplevel.fa : raw genomic sequence
  • $SPECIES_RSAT_ID.dna_rm.genome.fa : repeat-hard-masked genomic sequence
  • $SPECIES_RSAT_ID.gtf : annotation file
  • $SPECIES_RSAT_ID.pep.all.fa : peptide sequences of CDS features

where SPECIES_RSAT_ID is a string identifying this organism and its annotation.

Note: parse-gtf takes also GFF3 files, but the script expects the .gtf extension

For instance, to install assembly Wm82.a2.v1 of Glycine max from JGI Phytozome, we could do:

cd $RSAT

SPECIES_RSAT_ID=Glycine_max.Wm82.a2.v1.JGI

mkdir -p $RSAT/data/genomes/${SPECIES_RSAT_ID}/genome
# put there those 4 files (dna.toplevel.fa,dna_rm.genome.fa,.gtf,.pep.all.fa)

make -f makefiles/ensemblgenomes_FTP_client.mk SPECIES=Glycine_max \
    SPECIES_DIR=/var/www/html/rsat/data/genomes/$SPECIES_RSAT_ID \
    SPECIES_RSAT_ID=$SPECIES_RSAT_ID TAXON_ID=3847 GTF_SOURCE=JGI \
    install_from_gtf

Note that TAXON_ID can be obtained at https://www.ncbi.nlm.nih.gov/taxonomy or with the following RSAT tool:

ncbi-taxonomy 'Glycine max'

The newly installed species will be added to $RSAT/data/supported_organisms.tab and should be listed with the following command-line:

supported-organisms