TCGA Setup Part 3: Simplified and Optimized ETL #7
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added 2 commits
October 5, 2024 13:39
BominRahmani
reviewed
Oct 8, 2024
| ``` | ||
| wget | ||
| unzip | ||
| java (openjdk-23) |
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Do you know which part of this java would be required for?
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It's required for running SnpEff. Check out the function annotate_vcf.
The openjdk-23 is the version of Java that I used to run this command. Earlier versions may not work (which will throw an error).
BominRahmani
approved these changes
Oct 15, 2024
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Looks good to me! Nice work with the documentation, made this pretty easy to follow along. I might look into trying to convert that annotate function to make use of a python library since it seems a bit overkill to use java, but thats for a separate PR and I can take that on if there is time.
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The set_tcga_data.py script is now functional!
It will download all data and reference files needed for the analysis.
It will also modify and prepare data for downstream analysis.
Just make sure to read the README to understand what is going on.