diff --git a/PTL1/Genomes/Scripts/wrapper_submit.sh b/PTL1/Genomes/Scripts/wrapper_submit.sh index 5013539..9f7abbc 100644 --- a/PTL1/Genomes/Scripts/wrapper_submit.sh +++ b/PTL1/Genomes/Scripts/wrapper_submit.sh @@ -12,3 +12,17 @@ # Start at script 1 and go through script 5 (the final script) using the Universal genetic code python3 Scripts/wrapper.py -1 1 -2 5 --cds Input -o Output --genetic_code Universal --databases Databases > log.out +parent='/EukPhylo/PTL1/Genomes/Scripts/' +out_dir='/Output_data' +in_dir='/Input_data' + +## EXAMPLE RUN COMMANDS BELOW + +# A simple run of part 1 +python3 ${parent}/wrapper.py \ + --first_script 1 \ + --last_script 5 \ + --cds ${in_dir} \ + --databases ${parent}Databases \ + --genetic_code Universal \ + --output ${out_dir} > Output.out