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Cleanup README.md #18

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May 31, 2024
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6 changes: 3 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,10 @@ Method to compute per-cell embeddings for all JUMP-CP data.

## How to use this method

In the instructions below we use this method via [Docstore](https://dockstore.org/) and [Terra](https://app.terra.bio/) to generate embeddings for one JUMP-CP plate. When tested in May of 2024, this example plate took less than 1 hour to process via the workflow and cost $3.
In the instructions below we use this method via [Docstore](https://dockstore.org/) and [Terra](https://app.terra.bio/) to generate embeddings for one plate from the `cpg0016-jump` [dataset](https://github.com/jump-cellpainting/datasets).
When tested in May 2024, this example plate took less than 1 hour to process via the workflow and cost $3.

1. Download to your local file system the file [single_plate_example_inputs.json](https://github.com/jump-cellpainting/embedder/blob/main/single_plate_example_inputs.json) which holds input parameters for an example JUMP-CP plate.
1. Download to your local file system the file [single_plate_example_inputs.json](single_plate_example_inputs.json) which holds input parameters for an example JUMP-CP plate.
2. Go to [https://dockstore.org/workflows/github.com/jump-cellpainting/embedder](https://dockstore.org/workflows/github.com/jump-cellpainting/embedder:main?tab=info) and click on `Launch with: Terra`.
3. Either create a new [Terra](https://app.terra.bio/) workspace or choose an existing workspace into which to import the workflow method. Either way, you will be automatically redirected to the Terra page for the newly imported workflow.
4. On the [Terra](https://app.terra.bio/) workflow page:
Expand All @@ -17,4 +18,3 @@ In the instructions below we use this method via [Docstore](https://dockstore.or
5. Click `Run Analysis`

When the workflow completes, Terra will send a notification email.

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