Get rid of Hardcoded paths #23
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mariacuria
reviewed
Dec 3, 2024
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"/data/shared/repos/biomuta-old/downloads" is a symlink to "/data/shared/biomuta/downloads", and "/data/shared/repos/biomuta-old/generated_datasets" is a symlink to "/data/shared/biomuta/generated/datasets".
mariacuria
requested changes
Dec 4, 2024
mariacuria
requested changes
Dec 5, 2024
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Could you please revert to using utils and call get_config() to get to the config file? I got this method from Sean, it allows me to avoid writing "with open <...> json.load" in every script.
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Refactored scripts where paths are replaced with those dynamically fetched from config.json
Made changes to below scripts:
Everything in /data/shared/repos/biomuta-old/pipeline/download_step1/cbioportal
Everything in /data/shared/repos/biomuta-old/pipeline/convert_step2/cbioportal
In /data/shared/repos/biomuta-old/pipeline/convert_step2/liftover:
1_chr_pos_to_bed.py
2_liftover.sh
Updated config.json with a clear naming structure for paths and the added new paths