Specifying site-wide application settings

To change the settings, click the Admin link, then click the Change Settings tab.

Email Server

Specifies the SMTP server to use for sending automatically-generated mail messages to users of SMRT Portal. Mail messages are generated when:

• Users register
• Users change their passwords
• Administrators create a new user
• Administrators reset a user's password

To specify the SMTP server

1. Enter the name of the SMTP server to use. Example: mail.domain.com.

2. (Optional) Enter the SMTP user name and password if your server requires it.

3. (Optional) Check Enable Transport Layer Security if your server requires it. (TLS is a protocol to send outgoing messages securely from a client to the email server. Click here for further details.)
4. Click Send Test Email. The system sends an email to the administrator currently logged in, using the SMTP server specified. For example, if the administrator's email is admin@domain.com, the default SMTP host is mail.domain.com.
5. Click Apply to make the server name permanent.

Instrument Web Services URI

A Universal Resource Identifier (URI) specifies the location of the PacBio RS instrument running the Instrument Control Web Services. The Web Services automatically generate a list of SMRT Cell input which can then be used as part of secondary analysis jobs. You can specify multiple URIs for multiple instruments.

Use the format http://<Instrument_Name>:<Port_Number> where

• The instrument name can be a numeric IP address or a string.
• The port number should be 8080, unless the instrument controller is running on a port other than the default.

Example: http://PRIMARY_HOST:8080.

To add an Instrument URI

1. Click Add.
2. Enter a URI, then click OK to make the instrument location permanent.
3. (Optional) Repeat steps 1-2 to add additional URIs for additional instruments.

Reference Sequence Dropbox Directory Path

Specifies the location where SMRT Portal looks for reference sequences to import.

• Click Apply to make the dropbox location permanent.

Job Import Dropbox Directory Path

Specifies the location where SMRT Portal looks for directories corresponding to SMRT Pipe jobs to import.

• Click Apply to make the dropbox location permanent.

Job Archive Folder Directory Path

Specifies the location where SMRT Portal moves archived jobs to, and restores archived jobs from. See Archiving and restoring jobs for details.

• Click Apply to make the location permanent.

Protocol Selector

Specifies whether or not the Protocol Selector displays for all SMRT Portal users. (The Protocol Selector helps new users to choose an appropriate protocol for their specific analysis.)