# BUSCO specific configuration
# It overrides default values in code and dataset cfg, and is overridden by arguments in command line
# Uncomment lines when appropriate
[busco]
# Input file
;in = ./sample_data/target.fa
# Run name, used in output files and folder
out = {sample}
# Where to store the output directory
out_path = {outpath}
# Path to the BUSCO dataset
lineage_path = {lineage_path}
# Which mode to run (genome / protein / transcriptome)
#mode = genome
# How many threads to use for multithreaded steps
#cpu = 1
# Domain for augustus retraining, eukaryota or prokaryota
# Do not change this unless you know exactly why !!!
;domain = eukaryota
# Force rewrite if files already exist (True/False)
;force = False
# Restart mode (True/False)
;restart = False
# Blast e-value
;evalue = 1e-3
# Species to use with augustus, for old datasets only
;species = fly
# Augustus extra parameters
# Use single quotes, like this: '--param1=1 --param2=2'
;augustus_parameters = ''
# Tmp folder
tmp_path = {tmp_path}
# How many candidate regions (contigs, scaffolds) to consider for each BUSCO
;limit = 3
# Augustus long mode for retraining (True/False)
;long = False
# Quiet mode (True/False)
;quiet = False
# Debug logs (True/False), it needs Quiet to be False
;debug = True
# tar gzip output files (True/False)
;gzip = False
# Force single core for the tblastn step
;blast_single_core = True

[tblastn]
path = {conda_bin_path}

[makeblastdb]
path = {conda_bin_path}

[augustus]
path = {conda_bin_path}

[etraining]
path = {conda_bin_path}

[gff2gbSmallDNA.pl]
path = {conda_bin_path}

[new_species.pl]
path = {conda_bin_path}

[optimize_augustus.pl]
path = {conda_bin_path}

[hmmsearch]
path = {conda_bin_path}

[Rscript]
path = {Rscript}
