How To

Mount External Storage to DRAGEN Server v4

The external storage server directory must be mounted to the DRAGEN server v4 . Mount the storage as follows.

1. Using a Secure Shell (SSH), log in to the DRAGEN server v4.

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=<userid of user read andwrite permissions to the mounted drive>,gid=<group id of the user> //<External Storage Server Fully Qualified Domain Name or IP Address>/<AbsolutePathToTheMountedDirectory>/ /mnt/<ici_mount>/

   • Replace <username> with the username 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=39456,gid=34569 '//server-abc-01/My_Team/Project/MountingFolder/'/mnt/<ici_mount>

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

• The DRAGEN server v4 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 - Local software 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 have all given all the ACL permissions(read,write,execute, change and delete) on the external share of the NFS storage that is being mounted on the DRAGEN server v4.

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.

Prepare USB compatible with DRAGEN v4 server(type xfs or ext4 only).

For MacOS

1. Open Terminal

2. Install Homebrew. If you donw have Homebrew installed, copy and paste the following into terminal: /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

3. Install e2fprogs and xfsprogs:

   Command: brew install e2fsprogs

   Command: brew install e2fsprogs

4. Insert and identify the USB Drive. After inserting your USB drive, list all disks to identify your USB drive: Command: diskutil list

5. Unmount the USB drive. Replace diskX with the disk identifier of your USB drive: Command: diskutil umountDisk /dev/diskX

6. Format the USB drive.

   To format as ext4: Command: sudo /usb/local/opt/e2fsprogs/sbin/mkfs.ext4 /dev/diskX

   To format as XFS: Command: sudo /usb/local/opt/e2fsprogs/sbin/mkfs.xfs /dev/diskX

On the DRAGEN server v4 , create the /media/usbinstall directory that is used for mounting the USB ( mkdir /media/usbinstall ).

Connect the USB drive to the DRAGEN server v4.

Run the following command to mount the USB drive partition that contains the five downloaded installer files to the DRAGEN server v4: mount / /media/usbinstall

Run the following command to make sure that the downloaded files have executable permissions: chmod +x *

For Windows OS

1. From your Windows machine, go to any free installation software which formats USB to ext4/xfs example: DiskGenius website and download the free version.

2. Insert the USB Drive into the Windows machine.

3. Launch the USB formatter software (example: DiskGenius) and locate the USB drive.

4. Select the USB drive and right-click on the partition of the USB drive. Select "Delete current Partitions" (if any partitions already exists).

5. Create a new partition. Right click on the unallocated space and select "Create New Partition".

6. Select File system type as ext4 or XFS. Name the parititon label as usbinstall.

7. Hit save all to confirm all changes.

For DRAGEN SERVER v4

1. Format a USB with the xfs or ext4 file system using the following commands.

2. Replace <xfs/ext4> with either xfs or ext4 depending on which file system you use.

3. Insert the USB drive into a PC with an OS that is compatible with xfs or ext4 (for example, Linux).

4. Run the lsblk -I 8 -d command to confirm the USB drive name.

5. Run the following command to format the drive.

6. Replace <sd?> with the name of the USB drive (for example, sdc). sudo mkfs -t <xfs/ext4> /dev/<sd?>

7. Run the following command to create a partition directory: fdisk /dev/<sd?#>

8. Make the partition in the correct format by replacing <sd?> with the name of the partition directory (for example, sdc1). mkfs.<xfs/ext4> /dev/<sd?#>

Host and Domain Name

The domain name server (DNS) registers the DRAGEN server v4 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 software section of Software Errors and Corrective Actions.

Remote PC to DRAGEN Server v4 If there is no DNS, you can connect to the DRAGEN server v4 from your PC or a remote PC with SSH. Make sure that the IP address and fully qualified domain name of the DRAGEN server v4 (for example,< DRAGEN server v4 IP address> < testserver.abc.com>) are added to the hosts file on the PC.For instructions, refer to Software Errors and Corrective Actions.

Get the UID:GID

On the storage where you have been added as a user with read/write permissions, login to its shell and enter: id Example: Storage server name: teststorage User name: jsmith ssh jsmith@teststorage 'Command: id jsmith' Output: uid = 112233(jsmith) gid=32000(Storage_Users)

If the mounted storage/partition is controlled by an Access Control List, then get the ID of the access list and enter the gid of the Access control list. You can get the GID of the ACL by using the getent command on the Storage server: Example: Storage server name: teststorage Storage Parition with ACl: TestCIFSwithACL User name: jsmith ssh jsmith@teststorage Command: getent group TestCIFSwithACL Example Output: TestCIFSwithACL:669933

Other way to check the UID:GID once the storage is mounted is on the command line enter the command: Command: stat -c %u:%g <Path/to/mountedstoragedrive> Example: stat -c %u:%g /mnt/<ici_mount>

Add Certificate to Trusted

Follow the below steps to add the ceriticate to the Trusted URLs such that the message 'Your connection is not private" does not appear in your browser. For Mac OS

• Launch the browser and enter the application URL FQDN or with the Static IP from the nohup.out file.

• In the browser URL box, click on Not secure and then select Certificate is not valid option. This opens the Certificate Viewer pop-up

• Click on the Details tab in the pop-up and the click on the Export button at the bottom right corner to export this ceritificate.

• Save the certificate on the laptop. This would have the name with a .pem extension.

• From search box in the Mac, open the Keychain Access.

• Click on the Certificates tab, then select System on the left pane.

• Drag and drop the exported certificate(.pem file). The system would prompt to enter the password in the Keychain access.

• Enter network/laptop password in the Keychain access. This will add the certificate under the System certificates.

• Right click on the listed certificate and select Get Info.

• Expand the Trust section and in the option 'When using this certificate', select Always trust option from the dropdown.

• Once you close this pop-up it would ask you to re-enter your network password to update the Keychain access settings. Enter the password.

Now once you launch the application from the browser, the message 'Your connection is not secured' will no longer appear.