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=AHWH11M1+AHWH13M7+AHWH9M5+BJCY3M3+BJSJS1M2+C57BLSB16+CCFM1025+FAHWH21M7+FBJCP1M6+FBJCP2M1+FBJHD5M2+FCQNA20M1+FFJFZ2M5+FFJND11M5+FFJND13M6+FFJND14_L2+FFJND26M5+FFJND6M1+FFJND7M7+FFJXM1M3+FFJXM2M1+FGZ18I1M1+FGZ18I1M6+FGZ18I2M1+FGZ19I1M4+FGZ19I1M6+FGZ19I2M1+FGZ23I1M6+FGZ23I2M1+FGZ35I1M1+FGZ35I2M1+FGZ39I2M1+FGZ39MM6+FGZ3I1M6+FGZ3I2M1+FGZ6I2M1+FGZ9I2M1+FHLJDQ3M5+FHNFQ22M5+FHNFQ23M3+FHNFQ49M1+FHNFQ4M7+FHNXY43M2+FHNXY48M6+FHuNMY8M2+FJND12M6+FJND2M11+FJSSZ5M9+FJSSZ6M10+FJSSZ8M2+FJSWX19M3+FJSWX22M4+FJSWX24M2+FJSWX28M1+FJSWX30M2+FJSWX38M7+FJSWX4M9+FJSWX5M4+FJSWX7M1+FJSZJ1M5+FJSZJ2M2+FNMHLBE8M6+FNMHLBE9M6+FNXHL2M2+FNXHL8M4+FQHXN5M2+FSHMX2M1+FSHXXA1M1+FWX346+FXJCJ32M7+FZJJH10M6+FZJJH9M2+GuXi201667+HeNJZ1M1+HeNJZ2M1+HeNJZ9M1+HNXY26M4+HNXY47M8+HuNan2016415+HuNan2016497+HuNCS1M5+HuNCS3M4+HuNCS6M1+JSSZ7M1+JSWX17M1+JSWX21M5+JSWX23M8+JSWX25M8+JSWX26M5+JSWX39M4+M207F01M63+NMGCF1M12+NMGEL2M1+R2_CDS+SHMX3M1+SXR13+XJCJ1041+XJCJ653+XJCJ951+ZJHZ13M2+ZJHZ24M9+ZJHZ3M2+ZJHZ7M2+ZJHZD20M12
nohup docker run –name=pgap –restart=always \
-v “${seq_dir}”:/input \
-v “${out_dir}”:/output \
-w /pgap kastman/pgap:1.12 \
perl ./PGAP.pl –strains $strains \
–input /input –output /output \
–cluster -pangenome -method GF –thread 45 –bootstrap 500 &