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29 lines
1009 B
Bash
29 lines
1009 B
Bash
#!/bin/bash
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## Last updated Jan 2025 by Auden Cote-L'Heureux
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## This script is intended to be used to process genomic CDS with EukPhylo part 1 on an HPC that uses the Slurm workload manager.
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## The first part of the script are Slurm-specific parameters that should be adjusted by users to fit their resource allocation
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## needs and restrictions, followed by some example commands taken from the GitHub Wiki, more detail for which can be found
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## here: https://github.com/Katzlab/EukPhylo/wiki/EukPhylo-Part-1:-GF-assignment
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## Example commands
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# A simple run that goes from script 1 to script 7 (the last script) using the Universal genetic code
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parent='/EukPhylo/PTL1/Transcriptomes/Scripts'
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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 1
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python3 ${parent}/wrapper.py \
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--first_script 1 \
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--last_script 7 \
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--assembled_transcripts ${in_dir} \
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--databases ${parent}Databases \
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-g Universal \
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--output ${out_dir} > Output.out
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