Init Job

Initialize a new bakta annotation job.

Method: POST

Request Body:

{
  "name": "string",
  "repliconTableType": "CSV"
}

The body contains a user-defined name and the type of the replicon table (either TSV or CSV).

Response Body:

{
  "job": {
    "jobID": "3fa85f64-5717-4562-b3fc-2c963f66afa6",
    "secret": "string"
  },
  "uploadLinkFasta": "string",
  "uploadLinkProdigal": "string",
  "uploadLinkReplicons": "string"
}

The job section of the response contains a UUIDv4 (jobID) and a corresponding secret, this must be stored and provided by all subsequent requests that are associated to this job.

The response also contains three pre-authenticated S3 Urls:

uploadLinkFasta should be used to upload the (fasta) sequence data for annotation. uploadLinkProdigal (optional) can be used to upload an additional prodigal training file uploadLinkReplicons (optional) should be used to upload a replicon table in tsv format that describes the provided replicons in the fasta input file

By issuing a PUT request with the associated data as body you can upload the necessary data needed for the initialization.

NOTE: Previous API versions required the upload of all three files (FASTA, prodigal.tf and replicons.tsv) even if they were not used, this is no longer necessary as long these are not used in the subsequent start request.

Full Example (cURL)

Init request:

curl -X 'POST' \
  'https://api.bakta.computational.bio/api/v1/job/init' \
  -H 'accept: application/json' \
  -H 'Content-Type: application/json' \
  -d '{
  "name": "test",
  "repliconTableType": "TSV"
}'

Note: These PUT requests require the @ symbol before the path to the file. This signalizes cURL to use the content of the file and not the filename as input / body of your request.

Put sequence data (required):

curl -X 'PUT' \
  '<uploadLinkFasta>' \
  --data-binary "@path/to/file.fasta"

Put prodigal training file (optional):

curl -X 'PUT' \
  '<uploadLinkProdigal>' \
  --data-binary "@path/to/file.tf"

Put replicon table (optional):

curl -X 'PUT' \
  '<uploadLinkReplicons>' \
  --data-binary "@path/to/file.tsv"