Instrument connection

This section provides guidance on connecting an instrument (Revio or Vega system) to SMRT Link v25.3 to enable users to start sequencing runs and ensure seamless data transfer following sequence completion and importation into SMRT Link to view run metrics.

The following procedure is available only for SMRT Link users whose role is Admin.

Storage considerations

If not done already, identify a location in the cloud or on your shared file system (NFS) where the instrument can transfer data. This location must be readable from the SMRT Link server.

Instrument	Storage Requirements
Revio system	Up to 78 TB/year Assuming 120 Gbp HiFi Yield (~60 GB file size) per SMRT Cell and 1,300 SMRT Cells per year.
Vega system	Up to 6 TB/year Assuming ~60 Gbp HiFi yield (~30 GB file size) per SMRT Cell and 200 SMRT Cells per year.

This location can be located on the same share as jobs_root, but should be considered separately with regard to storage needs.
Job storage requirements depend on utilization and analyses performed.

Setting up a file transfer scheme/location

Step	Action
1	Identify the location on you SMRT Link or file share (NFS) where data should transfer
2	In SMRT Link web interface, navigate to `Settings > Instrument Settings`
3	Click `+ New File Transfer Location`
4	Choose the desired scheme: ssh (srs) Amazon S3 Google Cloud Storage Microsoft Azure Blob Storage S3-compatible storage
5	Enter the required information for the selected transfer scheme. Name: User-specified text string that displays in the Data directory dialog to identify the transfer scheme. Description: User-specified text string that describes the transfer scheme. Scheme-specific fields (see below).
6	Click `Save`
7	Once the transfer scheme is associated with a connected instrument (see Connect a New Instrument), return to this menu and click `Test Settings` to ensure that the scheme works.

Warning

The rsync daemon file transfer scheme will be disabled through a future software update in favor of more secure alternatives. Once disabled, file transfers will fail. PacBio strongly recommends transitioning to a supported transfer option.

Scheme-specific fields

SSH (srs)

Expand scheme details

Note

If you are using the SSH (srs) scheme, contact your Field Service Engineer (FSE) or PacBio tech support to have an SSH key created on your instrument. You will recieve the public SSH key which should be placed in ~/.ssh/authorized_keys file on the transfer server for whatever user is recieving the transfer (typically $SMRT_USER; Username setting below)

Please ensure that the ~/.ssh folder and ~/.ssh/authorized_keys file have the correct permissions set to allow the instrument to transfer data.

chmod 700 ~/.ssh
chmod 600 ~/.ssh/authorized_keys

Host: DNS name or IP address of your storage server. This may be the SMRT Link server or another storage location on the network. The name of this system can be obtained from your system administrator. Example: mp-srs.
Destination path: File system location that contains all data transferred via srs.
(Optional) Relative path: Path used to place run data in a specific sub- directory underneath the location specified in Destination path, on a per-instrument basis. A common value for this field is the instrument serial number or name. This field can contain only alphanumerics, “-“, “_”, and “/”. This field allows separation of run data from different instruments, which allows for easier location of particular run data when browsing the file system.
Username: Name of the service account used for transferring datasets to the remote file server.
SSH Key: Full path to the SSH private key on the instrument. Please contact your FSE or PacBio tech support to recieve this path.

Amazon S3

Expand scheme details

Bucket: Bucket name without the “s3://” prefix. Example: mp-s3

Region: Region where the bucket is hosted. To find your region run:

curl --silent --head https://s3.amazonaws.com/<your-bucket> | grep 'x-amz-bucket-region'

Path (Optional): Path used to place run data in a specific sub- directory within the specified bucket. This field can contain only alphanumerics, “-“, “_”, and “/”. This field allows separation of run data from different instruments, which allows for easier location of particular run data when browsing the file system.
Access key ID
Secret access key

S3 Bucket configuration

Create a private S3 bucket, e.g. mylabname-pacbio-instrument-data in your preferred geographical region.
Create an IAM policy pacbio-instrument-file-transfer granting the necessary permissions on the bucket, including the ability to read, write, and delete objects.
Create an IAM user with the new policy attached.
Create static access credentials for the new IAM user and save them for step 5.

Log in to SMRT Link as an admin user, navigate to Instrument Settings, and create a new Amazon S3 transfer scheme with the bucket name and region from step 1, and access credentials from step 4. Example IAM policy, where $BUCKET is replaced by the actual destination bucket name (e.g. mylabname-pacbio-instrument-data).

{
  "Version": "2012-10-17",
  "Statement": [
    {
      "Sid": "VisualEditor0",
      "Effect": "Allow",
      "Action": [
        "s3:PutObject",
        "s3:GetObject",
        "s3:GetBucketWebsite",
        "s3:GetObjectVersionTagging",
        "s3:ListBucketVersions",
        "s3:GetObjectAttributes",
        "s3:GetObjectTagging",
        "s3:ListBucket",
        "s3:GetBucketVersioning",
        "s3:GetObjectVersionAttributes",
        "s3:GetObjectVersion",
        "s3:DeleteObject"
      ],
      "Resource": [
        "arn:aws:s3:::$BUCKET",
        "arn:aws:s3:::$BUCKET/*"
      ]
    }
  ]
}

Google Cloud Storage

Expand scheme details

Bucket: Bucket name with no “gs://” prefix
Path: /path/to/subfolder in bucket to which to post
Access key: Create HMAC key in GCP console (see https://cloud.google.com/storage/docs/authentication/managing-hmackeys#console)
Secret key: Create HMAC key in GCP console (see https://cloud.google.com/storage/docs/authentication/managing-hmackeys#console)

Microsoft Azure Blob Storage

Expand scheme details

Account name: Account name, for example from https://.blob.core.windows.net
Container: The container name from https://.blob.core.windows.net/
Path: /path/to/subfolder in container
Account key: Key associated with account

S3-compatible storage

Expand scheme details

Note

Follow Amazon S3 Bucket configuration requirements when setting up S3 compatible storage.

Endpoint: URL for object storage endpoint, for example https://storage.googleapi.com
Bucket: Bucket name with no prefix, for example /bucketname .
Region (Optional): Region name for cloud-based services.
Path (Optional): Path used to place run data in a specific sub- directory underneath the location specified by your Bucket, on a per-instrument basis. A common value for this field is the instrument serial number or name. This field can contain only alphanumerics, “-“, “_”, and “/”. This field allows separation of run data from different instruments, which allows for easier location of particular run data when browsing the file system.
Access key: Access key for cloud-based services.
Secret key: Secret key for cloud-based services

Connect a new instrument

Note

The following procedure is available only for SMRT Link users whose role is Admin.

Step	Action
1	In SMRT Link web interface, navigate to `Settings > Instrument Settings`
2	Click `+ Connect New Instrument.`

3	Enter the IP address of the new Revio or Vega system. This is available on the instrument touchscreen; please write it down for later reference.
4	Enter the Instrument Secret Key. This is available on the instrument touchscreen, please write it down for later reference. Then, click `Continue`.

5	Enter the name of the new instrument, then click `Continue`. Note: The name must contain only alphanumeric characters, spaces, hyphens (-), underscores (_), or apostrophes ('). In addition, the instrument name must be unique for a given SMRT Link installation. Recommend using the instrument serial number (Revio: 84###; Vega: 21###)

6	Select a File Transfer Location. See Setting up a File Transfer Scheme/Location.

7	Click `Continue`
7	Verify the information, click `Confirm`, and then `Close`. The new instrument displays in the `Instrument Management` table as well as in the `Instruments` module

Modifying an existing instrument connection

Note

The following procedure is available only for SMRT Link users whose role is Admin.

Step	Action
1	In SMRT Link web interface, navigate to `Settings > Instrument Settings`
2	In the Instrument Management table, click an existing instrument. The Edit Instrument dialog displays
3	(Optional) Edit the instrument name. Note: The name must contain only alphanumeric characters, spaces, hyphens (-), underscores (_), or apostrophes (').
4	(Optional) Select a different File Transfer Location. Note: If a run is currently in progress, the file transfer location will be updated after the run is completed.
5	Click Apply