Allow for cloud uri (GCS) as input to the pipeline #42
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
snakemake gs plugin was failing when retrieving data, and very slow)
* changes to avoid copy from gcs will read tif files directly from cloud, both for metadata and for dask array creation.
remove print debug statements
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This adds support for inputs coming from a GCS bucket. It copies the entire dataset locally (as
temp()) for using it, and requires the gcloud CLI to be installed, as copying withgcloud storage cpwas far faster than whatever the snakemake gcs remote plugin was doing.This is mainly used for execution on coiled, for which wrapper (being developed in a separate repo) makes use of.
Note: does not support tar files in the cloud, only folders containing the tif files.