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broadinstitute / 2022_PERISCOPE

This repository contains all supporting analyses and files for Ramezani, Bauman, Singh, and Weisbart, et al. "A genome-wide atlas of human cell morphology".
BSD 3-Clause "New" or "Revised" License
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Issues with S3 download commands #23

Closed nmra-abarthmaron closed 1 year ago

nmra-abarthmaron commented 1 year ago

I found that using at least some of the download commands (e.g., the ones here) were not working for me.

Apologies if this issue is specific to me, but I found that adding wildcards at the beginning of the include strings helped solve the issue. (which could be due to hidden characters or filepath concatenation?) e.g.: "*20210422_6W_CP257_guide_normalized_feature_select_median_merged_ALLBATCHES___*" instead of: "20210422_6W_CP257_guide_normalized_feature_select_median_merged_ALLBATCHES___*"

I also noticed a typo in the A549 aggregated profile csvs. They are 20200805_A549_WG_Screen_guide_normalized_featureselectmerged_median_ rather than 20200805_A549_WG_Screen_guide_normalized_featureselectmedian_merged_

thanks!

ErinWeisbart commented 1 year ago

Thanks for catching those!

We re-organized our files a bit after writing documentation and apparently missed updating a couple paths. I've updated the READMEs to reflect the errors you caught.

File names should be consistently median_merged so I've updated the notebook and file paths in S3 to match.

nmra-abarthmaron commented 1 year ago

np, thanks for updating! overall the documentation and organization is super nice and easy to follow!