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23 lines
992 B
Bash
23 lines
992 B
Bash
#!/bin/bash
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## Last updated Jan 2025 by Auden Cote-L'Heureux; modified Feb 2025 by Adri K. Grow
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## This shell script is used for running EukPhylo part 2, and includes a general setup for use on an HPC that uses
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## the Slurm workload manager. It also includes several example run commands, which correspond to examples explained in more detail in the
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## EukPhylo Wiki (https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop).
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## These run commands can also be copied and run in the terminal / command line separately, without a shell script.
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parent='/EukPhylo/PTL2'
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out_dir='/Output_data'
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in_dir='/Input_data'
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## EXAMPLE RUN COMMANDS BELOW
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# A simple run of part 2, starting from ReadyToGo files and running through tree building
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python3 ${parent}/Scripts/eukphylo.py \
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--start raw \
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--end trees \
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--gf_list ${parent}listofOGs.txt \
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--taxon_list ${parent}taxon_list.txt \
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--data ${in_dir} \
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--output ${out_dir} > Output.out
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