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ingest: Upload NCBI/Andersen lab outputs to S3 #41

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joverlee521 opened this issue May 30, 2024 · 0 comments · Fixed by #47
Closed

ingest: Upload NCBI/Andersen lab outputs to S3 #41

joverlee521 opened this issue May 30, 2024 · 0 comments · Fixed by #47
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joverlee521 commented May 30, 2024

Follow up to #40

I'm planning to pull out the S3 related rules from upload_from_fauna and make them data source agnostic so that they can be used for fauna, ncbi, and andersen-lab ingest workflows.

I'm planning on uploading to the usual public S3 bucket since the NCBI data is public.
Both the NCBI data and Andersen lab data are currently specific to H5N1, so using the prefix
s3://nextstrain-data/files/workflows/avian-flu/h5n1/

data source type S3 URL
NCBI metadata s3://nextstrain-data/files/workflows/avian-flu/h5n1/ncbi/metadata.tsv.zst
sequences s3://nextstrain-data/files/workflows/avian-flu/h5n1/ncbi/ha/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/ncbi/mp/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/ncbi/na/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/ncbi/np/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/ncbi/ns/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/ncbi/pa/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/ncbi/pb1/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/ncbi/pb2/sequences.fasta.zst
Andersen Lab metadata s3://nextstrain-data/files/workflows/avian-flu/h5n1/andersen-lab/metadata.tsv.zst
sequences s3://nextstrain-data/files/workflows/avian-flu/h5n1/andersen-lab/ha/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/andersen-lab/mp/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/andersen-lab/na/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/andersen-lab/np/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/andersen-lab/ns/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/andersen-lab/pa/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/andersen-lab/pb1/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/andersen-lab/pb2/sequences.fasta.zst
merged metadata s3://nextstrain-data/files/workflows/avian-flu/h5n1/metadata.tsv.zst
sequences s3://nextstrain-data/files/workflows/avian-flu/h5n1/ha/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/mp/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/na/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/np/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/ns/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/pa/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/pb1/sequences.fasta.zst
s3://nextstrain-data/files/workflows/avian-flu/h5n1/pb2/sequences.fasta.zst

Note: The "merged" files will be blocked by #42, but I at least wanted to get the planned S3 URLs out here in case anyone disagrees with the paths.

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