Ranger DTL on ACCESS 2.0 Phylogenetic tree-based annotation of proteins Bansal MS, Kellis M, Kordi M, and Kundu S. Bansal MS, Kellis M, Kordi M, Kundu S. RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss. Bioinformatics. 2018 Sep 15;34(18):3214-3216. doi: 10.1093/bioinformatics/bty314. PMID: 29688310; PMCID: PMC6137995. Phylogeny / Annotation ranger_dtl_xsede ranger_dtl_comet perl "" 0 number_threads 2 perl $num_cpus < 24 scheduler.conf perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=$num_cpus\\n" number_threads2 2 perl $num_cpus == 24 scheduler.conf perl "nodes=1\\n" . "node_exclusive=1\\n" . "threads_per_process=24\\n" invoke_rangerdtl 5 perl $which_ranger == 1 perl "/projects/ps-ngbt/opt/comet/ranger_dtl/Linux/CorePrograms/Ranger-DTL.linux" invoke_rangerdtl2 5 perl $which_ranger == 2 perl "/projects/ps-ngbt/opt/comet/ranger_dtl/Linux/CorePrograms/AggregateRanger.linux" invoke_rangerdtl3 5 perl $which_ranger == 3 perl "/projects/ps-ngbt/opt/comet/ranger_dtl/Linux/SupplementaryPrograms/Ranger-DTL-Dated.linux" infile Input File (query) perl "-i ranger_dtl.infile" 10 ranger_dtl.infile all_results * runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours) perl "runhours=$value\\n" 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 The maximum hours to run must be greater than 0.05 perl $runtime < 0.05 The job will run on $num_cpus processors as configured. If it runs for the entire configured time, it will consume num_cpus X $runtime cpu hours perl $runtime > 0 Estimate the maximum time your job will need to run. We recommend testing initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. which_ranger Choose your Ranger Option 1 2 3 1 Please choose a Ranger option perl !defined $which_ranger 4 num_cpus How many cpus? 1 25 Please enter a number of threads 1-24 perl !defined $num_cpus Please enter a number of threads 24 or less perl $num_cpus > 24 Please enter a number of threads 1 or more perl $num_cpus < 1 output_name Name your output file perl "-o sample.1.out" sample1.out 20 Please specify your output file name perl !defined $output_name specify_dupcost Set Duplication Cost (-D) perl ($value ne $vdef) ? "-D $value":"" 2 4 specify_transfcost Set Transfer Cost (-T) perl ($value ne $vdef) ? "-T $value":"" 3 4 specify_losscost Set Loss Cost (-L) perl ($value ne $vdef) ? "-L $value":"" 1 4 specify_transftype Type of transfer cost to use (--type) 0 1 2 perl "--type $value" 7 threshold_value Threshold value for use with types 1 and 2 (--thr) perl defined $specify_transtype && $specify_transtype > 0 perl (defined $value) ? "--thr $value":"" 10 10 add_wholenumber Additional transfer cost for use with types 1 and 2 (--add) perl defined $specify_transtype && $specify_transtype > 0 10 perl (defined $value) ? "--add $value":"" specify_seed Set a user defined random number seed (--seed) perl (defined $value) ? "--seed $value" : "" 10 set_quiet No process output (--quiet) perl ($value) ? "--quiet" : "" 10 specify_summary Provide only output summary statistics (--summary) perl ($value) ? "--summary":"" 10