linguopeng/pgap repository overview

seq_dir=/home/data/ssy051/container/pgap/input # PGAP-formatted input files out_dir=/home/data/ssy051/container/pgap/output # Output directory (should exist) strains=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_2016+A14+A13+FSCPS14M2+FYNDL22M6

nohup docker run –name=pgap –restart=always
-v “${seq_dir}”:/input
-v “${out_dir}”:/output
-w /pgap linguopeng/pgap
perl ./PGAP.pl –strains $strains
–input /input –output /output
–cluster -pangenome -method GF –thread 45 –bootstrap 500 &