Create a batch file for simple BeadChip accessioning to Illumina Microarray Analytics PGx Analysis

BeadChip DMAP files must be accessioned to Illumina Connected Analytics (ICA) prior to sending data to ICA during scanning on the iScan. The data from the scanner is automatically sent to ICA for cloud-based analysis of array data using the Illumina Microarray Analytics PGx Analysis software. The accessioning can be done manually using the ICA command-line tool and following the “Accession BeadChips” instructions on the Illumina website, here. Alternatively, users can simplify the process by creating a batch (.bat) file. A batch file is a script file that contains a series of commands to be executed by a command-line interpreter application, eg, Command Prompt, in the Microsoft Windows operating system. Using a batch file saves time by automating tasks and allows for “push-button” accessioning of BeadChips for subsequent scans.

Whether created manually or using the .bat file, the command parses the DMAPs and moves them to one of two locations set by the user. The command requires three file paths:

• The folder containing locally saved DMAP files.

• The folder where successfully accessioned DMAP files are moved, eg, “Successfully Accessioned BeadChips.”

• The folder where unsuccessfully accessioned DMAP files are moved, eg, “Unsuccessfully Accessioned BeadChips.”

The folders for the parsed DMAP files must be created before running the command.

The instructions below detail how to create a batch file. The template used contains all the required commands; users need to add only the specific file paths and credentials to create a functioning .bat file. These steps assume access to ICA and that the Command Line Interface (CLI) executable file has been downloaded from the ICA support site.

Support Resources

Illumina Connected Analytics

Illumina Microarray Analytics PGx Analysis

Procedure

1. Open a text editor, eg, Notepad, and create a new text file in a convenient location1.

2. Name the newly created text file AccessionBeadChips.txt.

3. Paste the text below into the text file and update the configuration accordingly between “Configuration Start” and “Configuration End.”

4. The domain, workgroup name (workgroupName), server url (serverUrl)2, and BeadChip directory (beadChipDirectory)3 (where the DMAPs are located) must be configured. ICA CLI path (icaCliPath) and single sign-on option (singleSignOn) may need to be updated based on the customer setup (see inline comments within the batch file).

5. Save the text file and exit the text editor.

6. Rename the text file from AccessionBeadChips.txt to AccessionBeadChips.bat.

7. Run the .bat file, enter username and password, and make sure that the command executes successfully using BeadChips. When run successfully:

• BeadChips are moved from the “BeadChip” directory to the “Success” directory under the “BeadChip” directory.

• The output will be successfully logged in the “create_beadchips” log file that is created under the “BeadChip” directory.

1 This file can be created in a folder that also contains the DMAP files, the Successfully Accessioned BeadChips folder, the Unsuccessfully Accessioned BeadChips folder, and the ICA CLI executable.

2 Refer to the list of Support Regions in the Illumina Knowledge article BaseSpace Sequence Hub server instances explained.

3 If the location of the DMAP files is a network directory, the Universal Naming Convention (UNC) file path in the form \server\share\folderContainingDMAPS is preferred.

For additional information or questions, contact [e-mail].

The following is the text to paste into .txt file:

::===============================================================

:: Accession BeadChips into Illumina Connected Analytics (ICA)

::===============================================================

rem ==================== Configuration Start ====================

set domain=YOUR_DOMAIN

set workgroupName=YOUR_WORKGROUP_NAME

set serverUrl=YOUR_REGION.platform.illumina.com

set beadChipDirectory=YOUR_BEADCHIP_DIRECTORY

@rem If ICA CLI is installed in a different location than this file,

@rem update this value

set icaCliPath=ica.exe

@rem If single sign on is enabled for your domain, set this to true

set singleSignOn=false

rem ====================== Configuration End =====================

rem Default ICA and accessioning values

set icaConfigDir=%userprofile%.ica

set accessionSuccessFolder=%beadChipDirectory%\Successfully Accessioned BeadChips

set accessionFailureFolder=%beadChipDirectory%\Unsuccessfully Accessioned BeadChips

set accessionLogFile=%beadChipDirectory%\create_beadchips_log.txt

@echo off

echo Log into ICA with username and password

rem Create/Update configuration file

call :createDirectory "%icaConfigDir%" "ica configuration folder"

(

echo domain: %domain%

echo server-url: %serverUrl%

) > "%icaConfigDir%\config.yaml"

rem Add single sign on flag if needed

if %singleSignOn% == true (set ssoFlag=--sso) else (set ssoFlag=)

@echo on

set /P username=Enter username (eg, [e-mail]):

"%icaCliPath%" login "%username%" --workgroup-name "%workgroupName%" %ssoFlag%

@echo off

echo.

echo If username and password incorrect close this window and retry otherwise...

pause

echo Accessioning BeadChips...

rem Create success and failure directories if required

call :createDirectory "%accessionSuccessFolder%" accessionSuccessFolder

call :createDirectory "%accessionFailureFolder%" accessionFailureFolder

@echo on

"%icaCliPath%" infinium beadchips create "%beadChipDirectory%" "%accessionSuccessFolder%" "%accessionFailureFolder%" --log-file "%accessionLogFile%"

@echo off

echo.

echo BeadChip accessioning completed. Examine the above output and accessioning logs for more details: %accessionLogFile%

pause

rem Function to create directory if it does not exist

:createDirectory

if not exist "%~1" (

echo Creating %~2 folder, %~1

mkdir "%~1"

)

goto:eof

For any feedback or questions regarding this article (Illumina Knowledge Article #5887), contact Illumina Technical Support [e-mail].