Process genomic data by using Cloud Life Sciences

Run the pipeline

To run the pipeline, complete the following steps:

1. Create a bucket where you store the BAI file. Buckets are the basic containers that hold your data in Cloud Storage. To create a bucket named PROJECT_ID-life-sciences, run the gcloud storage buckets create command:

   gcloud storage buckets create gs://PROJECT_ID-life-sciences

   Replace PROJECT_ID with your Google Cloud project ID. You must use a globally unique bucket name.

   See bucket naming requirements.

   • Bucket names can only contain lowercase letters, numeric characters, dashes (-), and underscores (_). Spaces are not allowed.
   • Bucket names must start and end with a number or letter.
   • Bucket names must contain 3-63 characters. Names containing dots can contain up to 222 characters, but each dot-separated component can be no longer than 63 characters.
   • Bucket names cannot be represented as an IP address in dotted-decimal notation (for example, 192.168.5.4).
   • Bucket names cannot begin with the "goog" prefix.
   • Bucket names cannot contain "google" or close misspellings, such as "g00gle".

   If successful, the command returns the following:

   Creating gs://PROJECT_ID-life-sciences

2. To start the pipeline, run the gcloud beta lifesciences pipelines run command:

   gcloud beta lifesciences pipelines run \
       --regions us-east1 \
       --command-line 'samtools index ${BAM} ${BAI}' \
       --docker-image "gcr.io/cloud-lifesciences/samtools" \
       --inputs BAM=gs://genomics-public-data/NA12878.chr20.sample.bam \
       --outputs BAI=gs://PROJECT_ID-life-sciences/NA12878.chr20.sample.bam.bai

   If successful, the command returns the following:

   Running [projects/PROJECT_ID/operations/OPERATION_ID]

   Note the OPERATION_ID, which you use in the next step.

3. To track the pipeline's status, run the gcloud beta lifesciences operations wait command. Replace OPERATION_ID with the value printed in the previous step. The pipeline takes a few minutes to finish.

   gcloud beta lifesciences operations wait OPERATION_ID

   After the operation finishes, it returns the following message:

   Waiting for [projects/PROJECT_ID/operations/OPERATION_ID]...done.

4. To verify that the BAI file was generated, run the gcloud storage ls command:

   gcloud storage ls gs://PROJECT_ID-life-sciences

   If successful, the command returns the following:

   gs://PROJECT_ID-life-sciences/NA12878.chr20.sample.bam.bai

You've run a pipeline using the Cloud Life Sciences API to create a BAI file from a BAM file. Use a genome viewer to examine the NA12878.chr20.sample.bam BAM file using the NA12878.chr20.sample.bam.bai index file.