Prerequisites

Before installing Connected Insights , make sure that the following prerequisites are met.

DRAGEN Server v4 with Oracle Linux 8

The preferred version of Oracle Linux 8 is preinstalled on the DRAGEN server. The DRAGEN server software pipeline is also included. For more information, refer to the Illumina DRAGEN Server Installation Guide (document #200015717) on the Illumina support site.

Access to the DRAGEN Server from the Command-Line Interface

To access the DRAGEN server and run commands from the command-line interface, you should be familiar with the Linux commands used to install the software, the annotations database, and the license file. You must have root or sudo privileges to run installation commands. You must also have information about the host name and domain name of the DRAGEN server.

External Storage Drive

The external storage drive connects to the DRAGEN server directly or through the network. The external storage drive is used by Connected Insights to read inputs and write outputs.

• For inputs, Connected Insights reads secondary analysis data (for example, VCF and BAM files).

• For outputs, Connected Insights writes analysis output data and backup files (for example, annotated VCF files, visualization files, andPDF report files).

The storage drive must support the CIFS/SMB or NFS protocols. The Connected Insights installer checks for a minimum 100 gigabytes (GB) of available storage space before starting the installation. The required disk space is estimated by calculating the Genome Equivalent Samples (the number of samples multiplied by 3 GB). Illumina recommends a network speed of 10 gigabits (Gb) per second and encrypting this storage drive to safeguard your data.

After installation, Connected Insights creates a non-root user called ici_user with uid=431 and gid=433. All Connected Insights services use this non-root user to read and write data to the local and external storage drives.

Mount External Storage to DRAGEN Server The external storage server directory must be mounted to the DRAGEN server . Mount the storage as follows.

1. Using a Secure Shell (SSH), log in to the DRAGEN server.

2. Run the following command: mkdir -p /mnt/<ici_mount>

   ❗ <ici_mount> is an example directory name and can be replaced. The directory name can include dash (-) and underscore (_) characters, but cannot include spaces or special characters.

3. If you are using CIFS/SMB share storage, run the following command: mount -t cifs -o rw,user=<username>,mfsymlinks,uid=431,gid=433 //<External Storage Server Fully Qualified Domain Name or IP Address>/<AbsolutePathToTheMountedDirectory>/ /mnt/<ici_mount>/

   • Replace <username> with the user name of an account with read and write permissions for the share network-mounted directory. For example:

     mount -t cifs -o rw,user=bsmith,mfsymlinks,uid=431,gid=433 '//server-abc-01/My_Team/Project/MountingFolder/'/mnt/<ici_mount>

   • The CIFS <username> is mapped to uid=431 and gid=433, which is the Connected Insights user.

❗ Before mounting the NFS share storage, the following requirements must be met:

• The DRAGEN server must be registered in the /etc/exports file of the NFS storage server. Make sure to confirm this registration with your IT support.

• Connected Insights needs a minimum of 755 permissions for the secondary analysis folder that is located or copied under the external storage drive mounted as the <ici_mount> directory.

• If you are using Access Control List (ACL), then your IT support must remove the ACL permissions on the external share of theNFS storage that is being mounted on the DRAGEN server.

1. If you are using NFS share storage, run the following commands: mount -t nfs <External Storage Server Fully Qualified Domain Name or IPAddress>:/<AbsolutePathToTheMountedDirectory>/ /mnt/<ici_mount> For example: mount -t nfs server-abc-01:/My_Team/Project/MountingFolder/ /mnt/<ici_mount> chmod 755 /mnt/<ici_mount>

2. Add the network share to the /etc/fstab file so that the mount is permanent when rebooting.

   • Use the vi /etc/fstab command to open the file in an editor.

   • Replace <username> with the username of an account with read and write permissions for the share network-mounted directory. For CIFS/SMB or NFS mounts, refer to the following examples:

     • CIFS/SMB://<External Storage Server Fully Qualified Domain Name or IPAddress>/<AbsolutePathToTheMountedDirectory>/ /mnt/<ici_mount> cifs rw,user=<username>,mfsymlinks,uid=431,gid=433 0 0

     • NFS: <External Storage Server Fully Qualified Domain Name or IPAddress>:/<AbsolutePathToTheMountedDirectory>/ /mnt/<ici_mount> nfs defaults 0 0

     ❗ All spaces (except for the space between 0 and 0) are tabs.

   • If there are issues with updating the CIFS/SMB or NFS mount, refer to Software Errors and Corrective Actions.

Host and Domain Name

The domain name server (DNS) registers the DRAGEN server with the domain and resolves the IP address. With DNS Server

Use the following commands to return the host name, domain name, and fully qualified domain name with a DNS server.

• hostname — This command returns the host name of the server. To set a host name, use the hostnamectl set-hostname<Hostname of the server> --static command. Make sure that only the host name is entered. Check the /etc/hostname file tomake sure that only the host name is displayed and not the fully qualified domain name. For example, if the host name is testserver , the /etc/hostname file must only contain testserver

• hostname -d — This command returns only the domain name. To make sure that only the domain name is returned, the /etc/resolv.conf file must contain the domain name ( search <domain name> ) and the DNS IP address ( nameserver <DNS IPaddress> ) as shown in the following example. Two DNS addresses can display: search <domain name> nameserver <DNS IP address> nameserver <DNS IP address>

• hostname -f— This command returns the fully qualified domain name (for example, testerver.abc.com).

❗ Make sure that the host name commands ( hostname, hostname -d, and hostname -f ) return the correct values. If these commands do not return the correct values, the installation fails.

If the correct values are not returned, refer to the Connected Insights - Local section of Software Errors and Corrective Actions. Without DNS Server Run the following commands to return the host name, domain name, and fully qualified domain name without a DNS server.

• hostname — This command returns the host name of the server. To set a host name, use the hostnamectl set-hostname<Hostname of the server> --static command. Make sure that only the host name is entered. After running the command,make sure that only the host name is present in the /etc/hostname file. For example, if the host name is testserver , the /etc/hostname file must only contain testserver

• hostname -d — This command returns the domain name. The /etc/resolv.conf file must be updated to contain the domain name of your choice and the localhost IP address so that it matches exactly as shown in the following example (only <domain name> can be different): search <domain name> nameserver 127.0.0.1 After updating the /etc/resolv.conf file, make sure that you save your changes.

• hostname -f — This command returns the fully qualified domain name. This domain name must be added to the /etc/hosts file so that it matches exactly as shown in the following example (only <DRAGENServerFullyQualifiedDomainName> and <DRAGENServerHostnameOnly> can be different): 127.0.0.1 <DRAGENServerFullyQualifiedDomainName> <DRAGENServerHostnameOnly> localhost ::1 localhost localhost.localdomain localhost6 localhost6.localdomain6 After updating the /etc/hosts file, save your changes. Remote PC to DRAGEN Server If there is no DNS, you can connect to the DRAGEN server from your PC or a remote PC with SSH. Make sure that the IP address and fully qualified domain name of the DRAGEN server (for example,< DRAGEN server IP address> < testserver.abc.com>) are added to the hosts file on the PC.For instructions, refer to Software Errors and Corrective Actions.

Download and Copy Installation Files to External Storage or USB Drive To install Connected Insights, five files are required: two installer files, a license file, and two Knowledge Base (KB) files.

• Connected Insights and Illumina Connected Annotations installer files — These two files are downloaded from the Illumina Connected Insights Software Downloads support page.

• Connected Insights license file — This file is provided by Illumina and is installed before signing into Connected Insights.

• JAX-CKB and CIViC KB files — These two files are downloadable links provided by Illumina

❗ To avoid errors during installation, make sure that the installers and license file use the *.run extension.

After downloading the five files, copy them to a directory mounted to the DRAGEN server. Use either an external storage or USB drive mounted directly to the DRAGEN server. Based on your installation method, copy the downloaded files to an external storage or USB drive as follows. Copy Files to External Storage Drive Create the icipackages directory within the mounted directory ( /mnt/<ici_mount>/ ), and then copy the files to the directory as follows.

1. Run the following command to open the /mnt/<ici_mount>/ directory: cd /mnt/<ici_mount>/

2. Run the following command to create a directory named icipackages in the /mnt/<ici_mount>/ directory: mkdir /mnt/<ici_mount>/icipackages

3. Copy the five downloaded files to /mnt/<ici_mount>/icipackages/.

4. Run the following two commands to access the directory that contains the downloaded files and to include executable permissions for those files: cd /mnt/<ici_mount>/ cd /mnt/<ici_mount>/ chmod +x "<ConnectedInsightsInstallerFileName>" "<AnnotationsInstallerFileName>" "<CKBFileName>" "<CIViCFileName>" "<LicenseFileName>"

Copy Files to USB Drive The USB drive must meet the following requirements:

• USB 3.0

• At least 150 GB of storage space

• xfs or ext4 file system

If there are USB formatting or partition creation issues, refer to the Connected Insights - Local section in Software Errors and Corrective Actions Create a partition, copy the files to the USB drive, and mount the partition to the DRAGEN server as follows.

1. On the USB drive (xfs or ext4), create a partition.

2. Copy the five downloaded files to the partition created on the USB drive.

3. On the DRAGEN server , create the /media/usbinstall directory that is used for mounting the USB ( mkdir /media/usbinstall ).

4. Connect the USB drive to the DRAGEN server .

5. Run the following command to mount the USB drive partition that contains the five downloaded installer files to the DRAGEN server: mount /<path to USB partition with downloaded files> /media/usbinstall

6. Run the following command to make sure that the downloaded files have executable permissions: chmod +x "<ConnectedInsightsInstallerFileName>" "<AnnotationsInstallerFileName>" "<CKBFileName>" "<CIViCFileName>" "<LicenseFileName>"