Local Software Install

Moving application install file to the server:

Via USB:

1. Run the following command:

   1. cd /

2. Run the following command to identify which USB ports are in use:

   1. lsblk -I 8 –d

3. Record the ports that are currently in use.

4. Run the following command to create the USB drive mount directory on the DRAGEN server:

   1. mkdir /media/usb

5. Connect the USB drive with the DRAGEN Protein Quantification Pipeline installer to the front of the DRAGEN server.

6. Run the following command to confirm the USB drive name and details:

   1. lsblk

7. INFO: The details include the name of the USB drive under the Name column (sda, sdb, sdc, or sdd). The partition name also displays under the drive name (for example, sdc1).

8. Compare the USB ports that display to the ports identified in step 4 and identify the new port that appears. This port is where the installation software is located.

9. Run the following command to mount the USB drive to the USB mount directory of the DRAGEN server:

   1. mount /dev/<port> /media/usb/

   2. For example: mount /dev/sdc1 /media/usb

10. Run the following command to find the SHA value in the installer file:

    1. head -n25 /media/usb/install_DRAGEN_Protein_Quantification_v<version>.run | grep '^SHA'

11. Review the following table for SHA values.\

    SW Version	SHA
    2.2.2	d1000ea10b7eb5483db776efbe4873e80533dd0e5f5d713339a89cf5e7ee1a2b

    1. WARNING: If the SHA values do not match, stop the installation and contact Illumina Technical Support.

12. Run the following command to make sure that the USB drive is mounted to the USB mount directory:

    1. lsblk -I 8 –d

13. Run the following command to confirm that install_DRAGEN_Protein_Quantification_v<version>.run is in the USB drive mount directory:

    1. ls /media/usb/

14. Run the following command to copy install_DRAGEN_Protein_Quantification_v <version>.run to the staging directory:

    1. cp /media/usb/install_DRAGEN_Protein_Quantification_v<version>.run /staging/

15. Unmount USB from mount directory:

    1. umount /dev/<usb partition name>

Via Cloud Download

1. Navigate to staging:

   1. cd /staging/

2. Download the installer from its online location

   1. curl <link>

Via Connected Server

1. Copy the installer from an attached server:

   1. cp <external location of installer>/install_DRAGEN_Protein_Quantification_v <version>.run /staging/

Installation of application:

1. Run the following command to change directories to staging:

   1. cd /staging/

2. If necessary, change the permissions on the .run file to that it is executable with the following command

   1. chmod +x install_DRAGEN_Protein_Quantification_v<version>.run

3. Run the following command to make a temporary directory and install the .run file:

   1. sudo ./install_DRAGEN_Protein_Quantification_v<version>.run --target /staging/

4. If DAM is not installed, run the following command:

   1. sudo ./dragen-app-manager-<version> --target /staging/

   2. sudo ./install_DRAGEN_Protein_Quantification_v<version>.run --target /staging/

5. Run the following command to show the contents of the /usr/local/bin/ directory:

   1. ls /usr/local/bin/

6. Make sure that the /usr/local/bin/ directory has the following scripts:

   1. check_DRAGEN_Protein_Quantification-<version>.sh

   2. uninstall_DRAGEN_Protein_Quantification_<version>.sh

   3. run_DRAGEN_Protein_Quantification_<version>.sh

7. While in /staging directory, run the following command to confirm that the installation is successful:

   1. check_DRAGEN_Protein_Quantification_<version>.sh

8. Run the following help command to display the command options:

   1. run_DRAGEN_Protein_Quantification_<version>.sh –h

9. Perform run mock test using the following command:

   1. run_DRAGEN_Protein_Quantification_<version>.sh --mock -r /staging/dragen-app-manager/applications/Illumina_DRAGEN_Protein_Quantification_<version>/resources/test-files/mock_run_folder/

10. Confirm that the output files are present in the folder that was created during the mock test.

11. If an error occurs during installation, uninstall and reinstall DRAGEN Protein Quantification Pipeline as follows.

    1. Run the uninstall_DRAGEN_Protein_Quantification_<version>.sh script.

    2. Make sure that the following message displays:

       1. Successfully uninstalled DRAGEN_Protein_Quantification scripts, test-data, and images.

    3. Confirm that install_DRAGEN_Protein_Quantification_v<version>.run is present in staging:

       1. ls /staging/

    4. Repeat the steps in this section to reinstall DRAGEN Protein Quantification Pipeline.

    5. If the reinstallation fails, redo steps to put the application installer on the server again.

       1. Unmount and reinsert USB, proceeding with the Via USB subsection from the Move application installer to server section (unmount using step 17 from the above section of the guide).

    6. Repeat steps in this section to reinstall DRAGEN Protein Quantification Pipeline.