example.ini

# parameters:
# $FASTA: sequences (REQUIRED; fasta file)
FASTA=Path/to/file.fasta

# $LVL: clustering level (integer). ex: 3 = 8 clusters, 4 = 16 clusters (default 5 (32 clusters))
LVL=5

# $OUT: Directory to output the clusters (default PWD) creates one if $OUT does not exist
OUT=path/to/outputDirectory

# $UNIREF90: path to the DIAMOND UNIREF90 database (REQUIRED)
UNIREF90="path/to/uniref90"

# $UNIREF100: path to the UNIREF100 taxonomy list (REQUIRED)
UNIREF100="path/to/uniref100.taxlist"

# $TAXDUMP: path to the NCBI taxonomy dump (REQUIRED)
TAXDUMP="path/to/taxdumpFiles"

# $TAXO_LVL: taxonomic level for the WR index (default: phylum)
TAXO_LVL="phylum"

# $WHITE_NAME: Name of the target taxon for the WR index (REQUIRED)
WHITE_NAME="Chordata"

# $T: number of threads (default 8)
T=8

# $AST: alignment score threshold for alignment correction. Default -1 value means not using it. To use it, use value over or equal to 0
AST=-1

# $UNCOMPRESSED: Where uncompressed files will be stored when the decompression is needed. By default, it will be in the $OUT/uncompressed directory. Will be removed at the end of the process. Uncomment it to set it. (OPTIONAL)
#UNCOMPRESSED="${OUT}/uncompressed"