Singularity recipe for UBCG (Up-to-date Bacterial Core Genes).
Clone this repository, put the files from UBCG (UBCG.jar, programPath, UBCG.hmm) in the cloned folder together with the ubcg.def and use the following command to create the singularity container:
sudo singularity build ubcg.sif ubcg.def
Call UBCG from the singularity using the command line:
singularity exec ubcg2.sif java -jar /programs/UBCG.jar extract -i input_genome_fasta_file -bcg_dir output_ubcg_folder -label organism_name
singularity exec ubcg2.sif java -jar /programs/UBCG.jar align -ucg_dir output_ubcg_folder -run_id mytest1 -leaf uid,label