Create upload.md

[shntnu]

3

[ErinWeisbart]

@shntnu Can you take a close look at this (at your convenience) and let me know if it's what you had in mind? Please note that:

• I abstracted all the cellpainting-gallery paths to s3://cellpainting-gallery/${PROJECT_DIRECTORY}/${PROJECT_NESTING} We don't really use these variable names in any of our public workflows, but it does match the folder structure/nomenclature in #2.
• 0. Set up AWS still needs to be written. I don't think that linking to the jump-cellpainting steps is sufficient as it hard codes jump in many places. I don't have a great grasp on credentials and permissions so I'm afraid I either need you to write this or talk me through it before I can write it.
• Do we need --request-payer requester and/or --metadata-directive REPLACE flags in commands? They are not currently there.

[shntnu]

Can you take a close look at this (at your convenience) and let me know if it's what you had in mind? Please note that:

It looks great!

• I abstracted all the cellpainting-gallery paths to s3://cellpainting-gallery/${PROJECT_DIRECTORY}/${PROJECT_NESTING} We don't really use these variable names in any of our public workflows, but it does match the folder structure/nomenclature in Create folder_structure.md #2.

Perfect!

• 0. Set up AWS still needs to be written. I don't think that linking to the jump-cellpainting steps is sufficient as it hard codes jump in many places. I don't have a great grasp on credentials and permissions so I'm afraid I either need you to write this or talk me through it before I can write it.

Yep – still figuring out this bit. I've added a preface: Note: At present, only a few individuals – those with access to instructions here – have the ability to upload data to s3://cellpainting-gallery.

• Do we need --request-payer requester and/or --metadata-directive REPLACE flags in commands? They are not currently there.

Hm, I think --metadata-directive REPLACE is needed but not --request-payer requester. Thanks for spotting it! I've added

All this LGTM!

Feel free to ask questions, if not, please go ahead and merge