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Updates for release
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‎NOTICE.md‎

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# NOTICES AND INFORMATION
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**Do Not Translate or Localize**
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This software incorporates material from third parties. Microsoft makes certain open source code available at [https://3rdpartysource.microsoft.com](https://3rdpartysource.microsoft.com), or you may send a check or money order for US $5.00, including the product name, the open source component name, and version number, to:
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Source Code Compliance Team
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Microsoft Corporation
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One Microsoft Way
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Redmond, WA 98052
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USA
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Notwithstanding any other terms, you may reverse engineer this software to the extent required to debug changes to any libraries licensed under the GNU Lesser General Public License.
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---
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## Component: **bgzip.exe**
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**Source:** https://www.htslib.org/doc/bgzip.html
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**License:** [MIT License](https://opensource.org/licenses/MIT)
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---
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## Component: **bwalib.lib** (BWA)
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**Source:** https://github.com/lh3/bwa
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**License:**
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- [GNU General Public License v3.0 (GPL-3.0)](https://www.gnu.org/licenses/gpl-3.0.html)
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- [MIT License (for components)](https://opensource.org/licenses/MIT)
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---
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## Component: **tabix.exe**
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**Source:** https://www.htslib.org/doc/tabix.html
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**License:**
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- [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0)
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- [MIT License (for components)](https://opensource.org/licenses/MIT)
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---
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## Component: **zulu8.84.0.15-ca-jdk8.0.442-win_x64.msi**
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**Source:** https://www.azul.com/downloads/?package=jdk#zulu
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**License:** [GPL v2 with Classpath Exception](https://openjdk.org/legal/gplv2+ce.html)
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---
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## Component: **gatk-package-distribution-3.5.jar**
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**Source:** https://gatk.broadinstitute.org/hc/en-us/articles/360045763652
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**License:** [GATK-Protected License (Broad Institute Terms)](https://gatk.broadinstitute.org/hc/en-us/articles/360045763652)
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‎README.md‎

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@@ -5,9 +5,7 @@ We recommend new and existing customers use the latest Microsoft OSS solutions i
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- [Cromwell on Azure](https://github.com/microsoft/CromwellOnAzure)
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- [GA4GH TES on Azure](https://github.com/microsoft/ga4gh-tes)
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# Update 1/23/2025
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`msgen.ps1` and `run-on-azure-vm.sh` are now code-complete for the release of the binary executables, except, the actual binaries have not been released yet, pending completion of internal reviews. Thus, the `msgen.ps1` script will fail when it attempts to download it. We will update this README when the binaries are available for download. Instructions are avaialble here: https://github.com/microsoft/msgen/wiki
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Instructions are available here: https://github.com/microsoft/msgen/wiki
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‎src/msgen.ps1‎

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@@ -4,7 +4,10 @@ param (
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[string]$outputUrlPrefix,
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[string]$identityResourceId,
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# Optional parameters for deleting the VM's resource group on completion
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# Optional parameters
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[string]$msgenDownloadUrl = "https://datasetmsgen.blob.core.windows.net/dataset/msgen-oss/msgen-oss.zip",
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# Optional parameters for deleting the VM's resource group on completion
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[string]$subscriptionId = $null,
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[string]$resourceGroupName = $null,
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[string]$vmName = $null
@@ -13,12 +16,23 @@ param (
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$ErrorActionPreference = "Stop"
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$azCopyDownloadUrl = "https://aka.ms/downloadazcopy-v10-windows"
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$azCopyInstallDir = "C:\azcopy"
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$tempDir = "D:\temp"
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$msgenDownloadUrl = "https://datasetmsgen.blob.core.windows.net/dataset/msgen-oss/msgen-oss.zip"
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$azCopyInstallDir = "C:\azcopy"
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$tempDir = $env:TEMP
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$hg38m1xUrl = "https://datasetmsgen.blob.core.windows.net/dataset/hg38m1x/*"
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$hg38m1xIdxUrl = "https://datasetmsgen.blob.core.windows.net/dataset/hg38m1x.idx/*"
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$logsZipPath = "$tempDir\logs\logs.zip"
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$dotnetRuntimeUrl = "https://builds.dotnet.microsoft.com/dotnet/Runtime/9.0.6/dotnet-runtime-9.0.6-win-x64.exe"
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$dotnetRuntimeInstallerPath = "$tempDir\dotnet-runtime-9.0.6-win-x64.exe"
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$javaInstallerBinaryName = "zulu8.84.0.15-ca-jdk8.0.442-win_x64.msi"
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$javaInstallerPath = "$tempDir\$javaInstallerBinaryName"
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$javaDownloadUrl = "https://cdn.azul.com/zulu/bin/zulu8.84.0.15-ca-jdk8.0.442-win_x64.msi"
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$defaultJavaPath = "C:\java\bin\java.exe"
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# Function to check if .NET 9 Runtime is installed
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function Is-DotNet9Installed {
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$runtimes = & dotnet --list-runtimes 2>$null
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return $runtimes -match "9\."
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}
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try {
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# Create directories if they don't exist
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# Download input files
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Write-Host "Authenticating AZCOPY with the user-assigned managed identity..."
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& "$azCopyInstallDir\azcopy.exe" login --identity --identity-resource-id $identityResourceId
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Write-Host "Downloading input files..."
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& "$azCopyInstallDir\azcopy.exe" cp $inputUrl1 "$tempDir\inputs"
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if (![string]::IsNullOrEmpty($inputUrl2)) {
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& "$azCopyInstallDir\azcopy.exe" cp $inputUrl2 "$tempDir\inputs"
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}
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if (!(Test-Path $defaultJavaPath)) {
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Write-Host "Java not found, downloading installer..."
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(New-Object Net.WebClient).DownloadFile($javaDownloadUrl, $javaInstallerPath)
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Write-Host "Installing Java..."
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Start-Process -FilePath "msiexec.exe" -ArgumentList "/quiet /i `"$javaInstallerPath`" INSTALLDIR=C:\java\" -Wait
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if ($LASTEXITCODE -ne 0) { throw "Java installation failed. Exit code: $LASTEXITCODE" }
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Write-Host "Java installed successfully."
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} else {
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Write-Host "Java is already installed."
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}
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# Download and unzip msgen-oss
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Write-Host "Downloading msgen-oss..."
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& "$azCopyInstallDir\azcopy.exe" cp $msgenDownloadUrl "$tempDir" --recursive
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Expand-Archive -Path "$tempDir\msgen-oss.zip" -DestinationPath "$tempDir\msgen" -Force
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# Download needed dotnet version
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if (Is-DotNet9Installed) {
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Write-Host ".NET 9 runtime is already installed." -ForegroundColor Green
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} else {
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Write-Host ".NET 9 runtime not found. Installing..." -ForegroundColor Yellow
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Invoke-WebRequest -Uri $dotnetRuntimeUrl -OutFile $dotnetRuntimeInstallerPath
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# Install silently (no UI)
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Start-Process -FilePath $dotnetRuntimeInstallerPath -ArgumentList "/install", "/quiet", "/norestart" -Wait
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# Clean up
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Remove-Item $dotnetRuntimeInstallerPath
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# Confirm installation
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if (Is-DotNet9Installed) {
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Write-Host ".NET 9 runtime was successfully installed." -ForegroundColor Green
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} else {
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Write-Host "Installation failed or .NET 9 runtime not detected." -ForegroundColor Red
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}
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}
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# Run msgen-oss
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Write-Host "Running msgen-oss..."
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& "$tempDir\msgen\msgen-oss.exe" $tempDir "$tempDir\inputs" "$tempDir\outputs" "$tempDir\logs" "$tempDir\resources" "R=hg38m1x;GERC=GVCF;BGZIP=True"
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Write-Host "Completed genomics successfully."
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# Delete VM resouce group if set
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if ($subscriptionId -ne $null -and $resourceGroupName -ne $null -and $vmName -ne $null) {
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Write-Host "Deleting this VM now..."
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} catch {
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Write-Host "An error occurred: $($_.Exception.Message)"
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exit 1
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}
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Write-Host "Installing Azure CLI..."
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# Delete VM resouce group if set
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if ($subscriptionId -ne $null -and $resourceGroupName -ne $null -and $vmName -ne $null) {
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Write-Host "Deleting this VM now..."
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# Azure CLI MSI installer URL
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$azureCliInstallerUrl = "https://aka.ms/installazurecliwindows"
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$installerPath = "$env:TEMP\AzureCLIInstaller.msi"
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Write-Host "Installing Azure CLI..."
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# Download Azure CLI installer using WebClient
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Write-Host "Downloading Azure CLI installer from $azureCliInstallerUrl..."
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$webClient = New-Object System.Net.WebClient
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$webClient.DownloadFile($azureCliInstallerUrl, $installerPath)
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# Azure CLI MSI installer URL
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$azureCliInstallerUrl = "https://aka.ms/installazurecliwindows"
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$installerPath = "$env:TEMP\AzureCLIInstaller.msi"
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# Install Azure CLI silently
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Write-Host "Installing Azure CLI..."
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Start-Process -FilePath "msiexec.exe" -ArgumentList "/I `"$installerPath`" /quiet /norestart" -Wait
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# Download Azure CLI installer using WebClient
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Write-Host "Downloading Azure CLI installer from $azureCliInstallerUrl..."
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$webClient = New-Object System.Net.WebClient
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$webClient.DownloadFile($azureCliInstallerUrl, $installerPath)
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# Cleanup the installer
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Remove-Item -Path $installerPath -Force
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Write-Host "Azure CLI installed successfully."
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# Install Azure CLI silently
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Write-Host "Installing Azure CLI..."
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Start-Process -FilePath "msiexec.exe" -ArgumentList "/I `"$installerPath`" /quiet /norestart" -Wait
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# Add Azure CLI to PATH
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$azPath = "C:\Program Files (x86)\Microsoft SDKs\Azure\CLI2\wbin"
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if (-not ($env:PATH -like "*$azPath*")) {
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$env:PATH += ";$azPath"
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}
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# Cleanup the installer
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Remove-Item -Path $installerPath -Force
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Write-Host "Azure CLI installed successfully."
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# Step 2: Authenticate using User Assigned Managed Identity (UAMI)
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Write-Host "Authenticating using User Assigned Managed Identity..."
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$loginResult = az login --identity --username $identityResourceId --query '[0].id' -o tsv
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# Add Azure CLI to PATH
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$azPath = "C:\Program Files (x86)\Microsoft SDKs\Azure\CLI2\wbin"
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if (-not ($env:PATH -like "*$azPath*")) {
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$env:PATH += ";$azPath"
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}
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if ($LASTEXITCODE -ne 0) {
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Write-Host "Failed to authenticate with the User Assigned Managed Identity. Exiting..."
142-
exit 1
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}
144-
Write-Host "Authentication successful."
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# Step 2: Authenticate using User Assigned Managed Identity (UAMI)
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Write-Host "Authenticating using User Assigned Managed Identity..."
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$loginResult = az login --identity --resource-id $identityResourceId --query '[0].id' -o tsv
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146-
az account set --subscription $subscriptionId
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if ($LASTEXITCODE -ne 0) {
194+
Write-Host "Failed to authenticate with the User Assigned Managed Identity. Exiting..."
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exit 1
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}
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Write-Host "Authentication successful."
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Write-Host "Deleting the VM's resource group..."
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az group delete --name $resourceGroupName --yes --no-wait
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az account set --subscription $subscriptionId
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151-
Write-Host "VM resource group deletion initiated. Everything complete."
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}
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} catch {
154-
Write-Host "An error occurred: $($_.Exception.Message)"
155-
exit 1
156-
}
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Write-Host "Deleting the VM's resource group..."
202+
az group delete --name $resourceGroupName --yes --no-wait
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Write-Host "VM resource group deletion initiated. Everything complete."
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}

‎src/run-on-azure-vm.sh‎

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#!/bin/bash
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set -e
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AZURE_LOCATION="${1:-westus}"
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STEM_NAME="${2:-msgen2025}"
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RESOURCE_GROUP="${3:-${STEM_NAME}-vm}"
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IDENTITY_RESOURCE_GROUP="${4:-${STEM_NAME}-identity}"
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IDENTITY_NAME="${5:-${STEM_NAME}-identity}"
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VM_SIZE="${6:-Standard_D64d_v5}"
10-
INPUT_URL1="${7}"
11-
INPUT_URL2="${8}"
12-
OUTPUT_URL_PREFIX="${9}"
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INPUT_URL1="${1}"
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INPUT_URL2="${2}"
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OUTPUT_URL_PREFIX="${3}"
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AZURE_LOCATION="${4:-westus2}"
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STEM_NAME="${5:-msgen2025}"
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RESOURCE_GROUP="${6:-${STEM_NAME}-vm}"
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IDENTITY_RESOURCE_GROUP="${7:-${STEM_NAME}-identity}"
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IDENTITY_NAME="${8:-${STEM_NAME}-identity}"
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VM_SIZE="${9:-Standard_D64d_v5}"
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1414
VM_NAME="${STEM_NAME}-vm"
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ADMIN_USERNAME="azureuser"
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PASSWORD="$(< /dev/urandom tr -dc 'A-Za-z0-9' | head -c 16)!"
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SCRIPT_URL="https://raw.githubusercontent.com/microsoft/msgen/refs/heads/main/src/msgen.ps1"
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SUBSCRIPTION_ID=$(az account show --query id -o tsv)
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MSGEN_BINARIES_URL="https://datasetmsgen.blob.core.windows.net/dataset/msgen-oss/msgen-oss.zip"
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SUBSCRIPTION_ID=$(az account show --query id -o tsv | tr -d '\r')
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cleanup() {
2222
read -p "Do you want to delete the resource group '$RESOURCE_GROUP'? (y/n): " CONFIRM
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5151
echo "Managed identity $IDENTITY_NAME already exists. Skipping creation."
5252
fi
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54-
IDENTITY_ID=$(az identity show --name "$IDENTITY_NAME" --resource-group "$IDENTITY_RESOURCE_GROUP" --query id -o tsv)
54+
IDENTITY_ID=$(az identity show --name "$IDENTITY_NAME" --resource-group "$IDENTITY_RESOURCE_GROUP" --query id -o tsv | tr -d '\r')
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echo "Assigning Contributor role to the managed identity for the resource group $RESOURCE_GROUP..."
57-
IDENTITY_OBJECT_ID=$(az identity show --name "$IDENTITY_NAME" --resource-group "$IDENTITY_RESOURCE_GROUP" --query principalId -o tsv)
57+
IDENTITY_OBJECT_ID=$(az identity show --name "$IDENTITY_NAME" --resource-group "$IDENTITY_RESOURCE_GROUP" --query principalId -o tsv | tr -d '\r')
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5959
# Assign the Contributor role using the object ID and specifying the principal type
6060
az role assignment create \
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7070
--sku 2022-datacenter-azure-edition \
7171
--architecture x64 \
7272
--all \
73-
--query "[?offer=='WindowsServer' && sku=='2022-datacenter-azure-edition'].{Version: version, URN: urn} | sort_by(@, &Version)[-1].URN" -o tsv)
73+
--query "[?offer=='WindowsServer' && sku=='2022-datacenter-azure-edition'].{Version: version, URN: urn} | sort_by(@, &Version)[-1].URN" -o tsv | tr -d '\r')
7474
echo "Selected image: $LATEST_IMAGE"
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7676
echo "Creating virtual machine $VM_NAME in resource group $RESOURCE_GROUP..."
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8686
--enable-vtpm
8787

8888

89-
VM_ID=$(az vm show --name "$VM_NAME" --resource-group "$RESOURCE_GROUP" --query id -o tsv)
89+
VM_ID=$(az vm show --name "$VM_NAME" --resource-group "$RESOURCE_GROUP" --query id -o tsv | tr -d '\r')
9090
echo "Assigning managed identity $IDENTITY_NAME to virtual machine $VM_NAME..."
9191
az vm identity assign --identities "$IDENTITY_ID" --ids "$VM_ID"
9292

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105105
fi
106106
COMMAND_TO_EXECUTE+=" -outputUrlPrefix $OUTPUT_URL_PREFIX"
107107
COMMAND_TO_EXECUTE+=" -identityResourceId $IDENTITY_ID"
108+
COMMAND_TO_EXECUTE+=" -msgenDownloadUrl $MSGEN_BINARIES_URL"
108109
COMMAND_TO_EXECUTE+=" -subscriptionId $SUBSCRIPTION_ID"
109110
COMMAND_TO_EXECUTE+=" -resourceGroupName $RESOURCE_GROUP"
110111
COMMAND_TO_EXECUTE+=" -vmName $VM_NAME"

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