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Update run_eukphylo.sh

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Added in the variables to the script to increase configurability.
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Damon-Lee Pointon 2025-02-25 10:15:05 +00:00 committed by GitHub
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PTL2/run_eukphylo.sh
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@ -6,10 +6,17 @@
## EukPhylo Wiki (https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop).
## These run commands can also be copied and run in the terminal / command line separately, without a shell script.
parent='/PhyloToL-6/PTL2'
out_dir='/Output_data'
in_dir='/Input_data'
## EXAMPLE RUN COMMANDS BELOW
# A simple run of part 2, starting from ReadyToGo files and running through tree building
python3 Scripts/eukphylo.py --start raw --end trees --gf_list listofOGs.txt --taxon_list taxon_list.txt --data Input_folder --output Output_folder > Output.out
python3 ${parent}Scripts/eukphylo.py \
--start raw \
--end trees \
--gf_list ${parent}listofOGs.txt \
--taxon_list ${parent}taxon_list.txt \
--data ${in_dir} \
--output ${out_dir} > Output.out