# 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 = ./sample_data # Path to the BUSCO dataset ;lineage_path = ./sample_data/example # Which mode to run (genome / protein / transcriptome) ;mode = genome # How many threads to use for multithreaded steps ;cpu = 40 # 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/ # 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 to tblastn path = /gscratch/srlab/programs/ncbi-blast-2.8.1+/bin/ [makeblastdb] # path to makeblastdb path = /gscratch/srlab/programs/ncbi-blast-2.8.1+/bin/ [augustus] # path to augustus path = /gscratch/srlab/programs/Augustus-3.3.2/bin [etraining] # path to augustus etraining path = /gscratch/srlab/programs/Augustus-3.3.2/bin # path to augustus perl scripts, redeclare it for each new script [gff2gbSmallDNA.pl] path = /gscratch/srlab/programs/Augustus-3.3.2/scripts [new_species.pl] path = /gscratch/srlab/programs/Augustus-3.3.2/scripts [optimize_augustus.pl] path = /gscratch/srlab/programs/Augustus-3.3.2/scripts [hmmsearch] # path to HMMsearch executable path = /gscratch/srlab/programs/hmmer-3.2.1/src/ [Rscript] # path to Rscript, if you wish to use the plot tool Rscript_path = /usr/bin/