Update for release 4.3.6

4.3.6/create-batch-task.sh

@@ -23,11 +23,11 @@ BATCH_C="<STORAGE ACCOUNT CONTAINER NAME>"
 SAS_EXPIRATION="<EXPIRATION DATE>"
 
 # Genomic hash-table tarball
-GENOME_URL="https://webdata.illumina.com/downloads/software/dragen/references/genome-files/hg38-alt_masked.cnv.graph.hla.rna-9-r3.0-1.tar"
+GENOME_URL="https://dragentestdata.blob.core.windows.net/reference-genomes/Hsapiens/hash-tables/hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1.tar.gz"
 # FastQ Sample 1
-FASTQ_1="https://ilmn-dragen-giab-samples.s3.amazonaws.com/WGS/precisionFDA_v2_HG002/HG002.novaseq.pcr-free.35x.R1.fastq.gz"
+FASTQ_1="https://dragentestdata.blob.core.windows.net/samples/wes/NA24385-AJ-Son-R1-NS_S33/NA24385-AJ-Son-R1-NS_S33_L001_R1_001.fastq.gz"
 # FastQ Sample 2
-FASTQ_2="https://ilmn-dragen-giab-samples.s3.amazonaws.com/WGS/precisionFDA_v2_HG002/HG002.novaseq.pcr-free.35x.R2.fastq.gz"
+FASTQ_2="https://dragentestdata.blob.core.windows.net/samples/wes/NA24385-AJ-Son-R1-NS_S33/NA24385-AJ-Son-R1-NS_S33_L001_R2_001.fastq.gz"
 # Associated RGSM
 RGSM="NA24385-AJ-Son-R1-NS_S33"
 # A unique id to assign to the batch task.

4.3.6/deployment-configurations.md

@@ -33,8 +33,8 @@ The ARM template takes the following input parameters:
 | `storageAccountName` | `prefix` + "storage" | Name for Azure Blob Storage account (Total of 3-24 alphanumeric characters including prefix) |
 | `storageSku` | Standard_LRS* | [Azure Storage SKU](https://docs.microsoft.com/en-us/rest/api/storagerp/srp_sku_types) |
 | `storageNewOrExisting` | new | Specify whether to use an existing storage account or create a new one (Allowed values: `new` or `existing`) |
-| `offerSku` | dragen-4-2 | SKU for the DRAGEN offer in the Marketplace |
-| `vmImageVersion` | 4.2.7 | DRAGEN version |
+| `offerSku` | dragen-4-3 | SKU for the DRAGEN offer in the Marketplace |
+| `vmImageVersion` | 4.3.6 | DRAGEN version |
 
 ***NOTE:** The "Premium" type SKUs are not currently supported by this offering.
 

4.3.6/deployment-test.md

@@ -226,8 +226,8 @@ with each of the sections described in detail above.
 {
     "id": "<TASK_ID>",
     "commandLine": "<COMMAND>",
-    "resourcesFiles": [<RESOURCE_FILES>],
-    "outputFiles": [<OUTPUT_FILES>]
+    "resourcesFiles": "<RESOURCE_FILES>",
+    "outputFiles": "<OUTPUT_FILES>"
 }
 ```
 
@@ -309,7 +309,7 @@ The `$COMMAND` variable is now interpolated in the `task.json` file below.
     "commandLine": "$COMMAND",
     "resourceFiles": [{
         "filePath": "dragen.tar",
-        "httpUrl": "https://dragentestdata.blob.core.windows.net/reference-genomes/Hsapiens/hash-tables/hg38-alt_masked.cnv.graph.hla.rna-9-r3.0-1.tar"
+        "httpUrl": "https://dragentestdata.blob.core.windows.net/reference-genomes/Hsapiens/hash-tables/hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1.tar.gz"
     }, {
         "filePath": "1.fq.gz",
         "httpUrl": "https://dragentestdata.blob.core.windows.net/samples/wes/NA24385-AJ-Son-R1-NS_S33/NA24385-AJ-Son-R1-NS_S33_L001_R1_001.fastq.gz"

4.3.6/feed.xml

@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.2.0">Jekyll</generator><link href="/feed.xml" rel="self" type="application/atom+xml" /><link href="/" rel="alternate" type="text/html" /><updated>2024-09-13T17:09:32+00:00</updated><id>/feed.xml</id><title type="html">DRAGEN on Azure</title><subtitle>Quickstart</subtitle></feed>
+<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.2.0">Jekyll</generator><link href="/feed.xml" rel="self" type="application/atom+xml" /><link href="/" rel="alternate" type="text/html" /><updated>2024-09-13T17:14:49+00:00</updated><id>/feed.xml</id><title type="html">DRAGEN on Azure</title><subtitle>Quickstart</subtitle></feed>

4.3.6/index.html

@@ -497,12 +497,12 @@ <h5 id="optional-parameters-default-values-are-set-but-can-be-overridden">Option
     </tr>
     <tr>
       <td><code class="language-plaintext highlighter-rouge">offerSku</code></td>
-      <td>dragen-4-2</td>
+      <td>dragen-4-3</td>
       <td>SKU for the DRAGEN offer in the Marketplace</td>
     </tr>
     <tr>
       <td><code class="language-plaintext highlighter-rouge">vmImageVersion</code></td>
-      <td>4.2.7</td>
+      <td>4.3.6</td>
       <td>DRAGEN version</td>
     </tr>
   </tbody>
@@ -817,8 +817,8 @@ <h4 id="taskjson">task.json</h4>
 <div class="language-json highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="p">{</span><span class="w">
     </span><span class="nl">"id"</span><span class="p">:</span><span class="w"> </span><span class="s2">"&lt;TASK_ID&gt;"</span><span class="p">,</span><span class="w">
     </span><span class="nl">"commandLine"</span><span class="p">:</span><span class="w"> </span><span class="s2">"&lt;COMMAND&gt;"</span><span class="p">,</span><span class="w">
-    </span><span class="nl">"resourcesFiles"</span><span class="p">:</span><span class="w"> </span><span class="p">[</span><span class="err">&lt;RESOURCE_FILES&gt;</span><span class="p">],</span><span class="w">
-    </span><span class="nl">"outputFiles"</span><span class="p">:</span><span class="w"> </span><span class="p">[</span><span class="err">&lt;OUTPUT_FILES&gt;</span><span class="p">]</span><span class="w">
+    </span><span class="nl">"resourcesFiles"</span><span class="p">:</span><span class="w"> </span><span class="s2">"&lt;RESOURCE_FILES&gt;"</span><span class="p">,</span><span class="w">
+    </span><span class="nl">"outputFiles"</span><span class="p">:</span><span class="w"> </span><span class="s2">"&lt;OUTPUT_FILES&gt;"</span><span class="w">
 </span><span class="p">}</span><span class="w">
 </span></code></pre></div></div>
 
@@ -902,7 +902,7 @@ <h5 id="create-taskjson">Create task.json</h5>
     </span><span class="nl">"commandLine"</span><span class="p">:</span><span class="w"> </span><span class="s2">"$COMMAND"</span><span class="p">,</span><span class="w">
     </span><span class="nl">"resourceFiles"</span><span class="p">:</span><span class="w"> </span><span class="p">[{</span><span class="w">
         </span><span class="nl">"filePath"</span><span class="p">:</span><span class="w"> </span><span class="s2">"dragen.tar"</span><span class="p">,</span><span class="w">
-        </span><span class="nl">"httpUrl"</span><span class="p">:</span><span class="w"> </span><span class="s2">"https://dragentestdata.blob.core.windows.net/reference-genomes/Hsapiens/hash-tables/hg38-alt_masked.cnv.graph.hla.rna-9-r3.0-1.tar"</span><span class="w">
+        </span><span class="nl">"httpUrl"</span><span class="p">:</span><span class="w"> </span><span class="s2">"https://dragentestdata.blob.core.windows.net/reference-genomes/Hsapiens/hash-tables/hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1.tar.gz"</span><span class="w">
     </span><span class="p">},</span><span class="w"> </span><span class="p">{</span><span class="w">
         </span><span class="nl">"filePath"</span><span class="p">:</span><span class="w"> </span><span class="s2">"1.fq.gz"</span><span class="p">,</span><span class="w">
         </span><span class="nl">"httpUrl"</span><span class="p">:</span><span class="w"> </span><span class="s2">"https://dragentestdata.blob.core.windows.net/samples/wes/NA24385-AJ-Son-R1-NS_S33/NA24385-AJ-Son-R1-NS_S33_L001_R1_001.fastq.gz"</span><span class="w">

4.3.6/mainTemplate.json

@@ -44,11 +44,11 @@
         },
         "offerSku": {
             "type": "string",
-            "defaultValue": "dragen-4-2"
+            "defaultValue": "dragen-4-3"
         },
         "vmImageVersion": {
             "type": "string",
-            "defaultValue": "4.2.7"
+            "defaultValue": "4.3.6"
         },
         "azureBatchServiceOid": {
             "type": "string"
@@ -202,6 +202,7 @@
         {
             "type": "Microsoft.Batch/batchAccounts/pools",
             "apiVersion": "2023-05-01",
+            "apiVersion": "2023-05-01",
             "name": "[concat(variables('batchAccountName'), '/', variables('batchPoolName'))]",
             "dependsOn": [
                 "[resourceId('Microsoft.Batch/batchAccounts', variables('batchAccountName'))]"

4.3.6/tutorial-docs/.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/3d/70297cd4a249a22b1f609c28e4a84955f8d9ffad8fc6a14508d65de8856c18 → 4.3.6/tutorial-docs/.jekyll-cache/Jekyll/Cache/Jekyll--Converters--Markdown/c9/ae43215797ddd973389c62c4a12ad76e3ac1b1b208d2a2c6eae391bb254b08

@@ -1,4 +1,4 @@
-I"�3

+I"�3

 <h2 id="introduction">Introduction</h2>
 
 <p>This Quick Start guide provides instructions and resources to guide users through deploying <a href="https://www.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html">Dynamic Read Analysis for GENomics (DRAGEN)</a> on Azure.  It is primarily intended for users who are interested in a quick and easy setup for running genomics workloads in the cloud.</p>
@@ -278,12 +278,12 @@ at the bottom of the screen and click <strong>Create</strong></li>
     </tr>
     <tr>
       <td><code class="language-plaintext highlighter-rouge">offerSku</code></td>
-      <td>dragen-4-2</td>
+      <td>dragen-4-3</td>
       <td>SKU for the DRAGEN offer in the Marketplace</td>
     </tr>
     <tr>
       <td><code class="language-plaintext highlighter-rouge">vmImageVersion</code></td>
-      <td>4.2.7</td>
+      <td>4.3.6</td>
       <td>DRAGEN version</td>
     </tr>
   </tbody>
@@ -598,8 +598,8 @@ with each of the sections described in detail above.</p>
 <div class="language-json highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="p">{</span><span class="w">
     </span><span class="nl">"id"</span><span class="p">:</span><span class="w"> </span><span class="s2">"&lt;TASK_ID&gt;"</span><span class="p">,</span><span class="w">
     </span><span class="nl">"commandLine"</span><span class="p">:</span><span class="w"> </span><span class="s2">"&lt;COMMAND&gt;"</span><span class="p">,</span><span class="w">
-    </span><span class="nl">"resourcesFiles"</span><span class="p">:</span><span class="w"> </span><span class="p">[</span><span class="err">&lt;RESOURCE_FILES&gt;</span><span class="p">],</span><span class="w">
-    </span><span class="nl">"outputFiles"</span><span class="p">:</span><span class="w"> </span><span class="p">[</span><span class="err">&lt;OUTPUT_FILES&gt;</span><span class="p">]</span><span class="w">
+    </span><span class="nl">"resourcesFiles"</span><span class="p">:</span><span class="w"> </span><span class="s2">"&lt;RESOURCE_FILES&gt;"</span><span class="p">,</span><span class="w">
+    </span><span class="nl">"outputFiles"</span><span class="p">:</span><span class="w"> </span><span class="s2">"&lt;OUTPUT_FILES&gt;"</span><span class="w">
 </span><span class="p">}</span><span class="w">
 </span></code></pre></div></div>
 
@@ -683,7 +683,7 @@ EOF
     </span><span class="nl">"commandLine"</span><span class="p">:</span><span class="w"> </span><span class="s2">"$COMMAND"</span><span class="p">,</span><span class="w">
     </span><span class="nl">"resourceFiles"</span><span class="p">:</span><span class="w"> </span><span class="p">[{</span><span class="w">
         </span><span class="nl">"filePath"</span><span class="p">:</span><span class="w"> </span><span class="s2">"dragen.tar"</span><span class="p">,</span><span class="w">
-        </span><span class="nl">"httpUrl"</span><span class="p">:</span><span class="w"> </span><span class="s2">"https://dragentestdata.blob.core.windows.net/reference-genomes/Hsapiens/hash-tables/hg38-alt_masked.cnv.graph.hla.rna-9-r3.0-1.tar"</span><span class="w">
+        </span><span class="nl">"httpUrl"</span><span class="p">:</span><span class="w"> </span><span class="s2">"https://dragentestdata.blob.core.windows.net/reference-genomes/Hsapiens/hash-tables/hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1.tar.gz"</span><span class="w">
     </span><span class="p">},</span><span class="w"> </span><span class="p">{</span><span class="w">
         </span><span class="nl">"filePath"</span><span class="p">:</span><span class="w"> </span><span class="s2">"1.fq.gz"</span><span class="p">,</span><span class="w">
         </span><span class="nl">"httpUrl"</span><span class="p">:</span><span class="w"> </span><span class="s2">"https://dragentestdata.blob.core.windows.net/samples/wes/NA24385-AJ-Son-R1-NS_S33/NA24385-AJ-Son-R1-NS_S33_L001_R1_001.fastq.gz"</span><span class="w">

4.3.6/tutorial-docs/deployment-configurations.md

@@ -33,8 +33,8 @@ The ARM template takes the following input parameters:
 | `storageAccountName` | `prefix` + "storage" | Name for Azure Blob Storage account (Total of 3-24 alphanumeric characters including prefix) |
 | `storageSku` | Standard_LRS* | [Azure Storage SKU](https://docs.microsoft.com/en-us/rest/api/storagerp/srp_sku_types) |
 | `storageNewOrExisting` | new | Specify whether to use an existing storage account or create a new one (Allowed values: `new` or `existing`) |
-| `offerSku` | dragen-4-2 | SKU for the DRAGEN offer in the Marketplace |
-| `vmImageVersion` | 4.2.7 | DRAGEN version |
+| `offerSku` | dragen-4-3 | SKU for the DRAGEN offer in the Marketplace |
+| `vmImageVersion` | 4.3.6 | DRAGEN version |
 
 ***NOTE:** The "Premium" type SKUs are not currently supported by this offering.
 

4.3.6/tutorial-docs/deployment-test.md

@@ -226,8 +226,8 @@ with each of the sections described in detail above.
 {
     "id": "<TASK_ID>",
     "commandLine": "<COMMAND>",
-    "resourcesFiles": [<RESOURCE_FILES>],
-    "outputFiles": [<OUTPUT_FILES>]
+    "resourcesFiles": "<RESOURCE_FILES>",
+    "outputFiles": "<OUTPUT_FILES>"
 }
 ```
 
@@ -309,7 +309,7 @@ The `$COMMAND` variable is now interpolated in the `task.json` file below.
     "commandLine": "$COMMAND",
     "resourceFiles": [{
         "filePath": "dragen.tar",
-        "httpUrl": "https://dragentestdata.blob.core.windows.net/reference-genomes/Hsapiens/hash-tables/hg38-alt_masked.cnv.graph.hla.rna-9-r3.0-1.tar"
+        "httpUrl": "https://dragentestdata.blob.core.windows.net/reference-genomes/Hsapiens/hash-tables/hg38-alt_masked.cnv.graph.hla.rna-10-r4.0-1.tar.gz"
     }, {
         "filePath": "1.fq.gz",
         "httpUrl": "https://dragentestdata.blob.core.windows.net/samples/wes/NA24385-AJ-Son-R1-NS_S33/NA24385-AJ-Son-R1-NS_S33_L001_R1_001.fastq.gz"