DEVEX-2420 Post release 2.11.9 (#482)

* DEVEX-2420 release 2.11.9 (feat) all - updt * DEVEX-2420 release 2.11.9 (fix) apps_2478_headJobOnDemand_subjob.wdl - update to the new instance specs * DEVEX-2420 release 2.11.9 (fix) all - update docker image due to "Error message from daemon: missing signature key" with the previous version of the image * DEVEX-2420 release 2.11.9 (fix) all - update docker image fixture * DEVEX-2420 release 2.11.9 (fix) dxapp.json - update instance types for the new org * DEVEX-2420 release 2.11.9 (feat) all - update
dnanexus · Nov 21, 2024 · 003687f · 003687f
1 parent 4cab3aa
commit 003687f
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diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -4,6 +4,11 @@
 
 ...
 
+## 2.11.9 2024-11-07
+
+* Added support for new region in AWS Bahrain
+* Added a deprecation note for dxCompiler Docker image in the Docker Hub
+
 ## 2.11.8 2024-10-22
 
 * Added [DIY Docker image instructions](./scripts/docker_image/). This replaces the Docker image published to Docker Hub, which is now deprecated.

diff --git a/compiler/src/main/resources/application.conf b/compiler/src/main/resources/application.conf
@@ -1,5 +1,5 @@
 dxCompiler {
-    version = "2.11.9-SNAPSHOT"
+    version = "2.11.10-SNAPSHOT"
 }
 
 #

diff --git a/compiler/src/test/resources/compiler/BroadGenomicsDocker.wdl b/compiler/src/test/resources/compiler/BroadGenomicsDocker.wdl
@@ -6,7 +6,7 @@ task BroadGenomicsDocker {
         sed 's/Version: //'
     }
     runtime {
-        docker: "broadinstitute/genomes-in-the-cloud:2.2.4-1469632282"
+        docker: "broadinstitute/genomes-in-the-cloud:2.2.5-1485277291"
         memory: "3 GB"
         cpu: "1"
         disks: "local-disk 10 HDD"

diff --git a/core/src/main/resources/application.conf b/core/src/main/resources/application.conf
@@ -1,5 +1,5 @@
 dxCompilerCore {
-    version = "2.11.9-SNAPSHOT"
+    version = "2.11.10-SNAPSHOT"
 }
 
 #

diff --git a/core/src/test/resources/compiler/BroadGenomicsDocker.wdl b/core/src/test/resources/compiler/BroadGenomicsDocker.wdl
@@ -6,7 +6,7 @@ task BroadGenomicsDocker {
         sed 's/Version: //'
     }
     runtime {
-        docker: "broadinstitute/genomes-in-the-cloud:2.2.4-1469632282"
+        docker: "broadinstitute/genomes-in-the-cloud:2.2.5-1485277291"
         memory: "3 GB"
         cpu: "1"
         disks: "local-disk 10 HDD"

diff --git a/dxcint/resources/expected_failure/bad_status.wdl b/dxcint/resources/expected_failure/bad_status.wdl
@@ -3,7 +3,7 @@ task BadCommand {
           ls /xx/yyy
       }
       runtime {
-          docker: "broadinstitute/genomes-in-the-cloud:2.2.4-1469632282"
+          docker: "broadinstitute/genomes-in-the-cloud:2.2.5-1485277291"
       }
       output {
           Int rc = 1

diff --git a/dxcint/resources/expected_output/advanced.wdl b/dxcint/resources/expected_output/advanced.wdl
@@ -9,7 +9,7 @@ task BroadGenomicsDocker {
     sed 's/Version: //'
   }
   runtime {
-      docker: "broadinstitute/genomes-in-the-cloud:2.2.4-1469632282"
+      docker: "broadinstitute/genomes-in-the-cloud:2.2.5-1485277291"
       memory: "3 GB"
       cpu: "1"
       disks: "local-disk 10 HDD"

diff --git a/dxcint/resources/expected_output/advanced_results.json b/dxcint/resources/expected_output/advanced_results.json
@@ -2,5 +2,5 @@
   "advanced.cgrep_count": [8, 0, 3],
   "advanced.str_animals_result" : "Arctic fox_family --K -S --flags --contamination 0 --s foobar",
   "advanced.str_animals_family" : "Family Arctic fox_family",
-  "advanced.BroadGenomicsDocker_version" : "0.7.13-r1126"
+  "advanced.BroadGenomicsDocker_version" : "0.7.15-r1140"
 }
diff --git a/dxcint/resources/extras_expected_flags/apps_2478_headJobOnDemand_subjob.wdl b/dxcint/resources/extras_expected_flags/apps_2478_headJobOnDemand_subjob.wdl
@@ -19,7 +19,7 @@ task apps_2478_headJobOnDemand_subjob_t01 {
         File fruits
     }
     # provide dynamical size of the disk
-    Int disk_req_gb = ceil(size(fruits, "GB")) + 50
+    Int disk_req_gb = ceil(size(fruits, "GB")) + 120
 
   command <<<
     lines=$(df -t btrfs | grep dev)

diff --git a/executorCommon/src/main/resources/application.conf b/executorCommon/src/main/resources/application.conf
@@ -1,5 +1,5 @@
 dxExecutorCommon {
-    version = "2.11.9-SNAPSHOT"
+    version = "2.11.10-SNAPSHOT"
 }
 
 #

diff --git a/executorCwl/src/main/resources/application.conf b/executorCwl/src/main/resources/application.conf
@@ -1,5 +1,5 @@
 dxExecutorCwl {
-    version = "2.11.9-SNAPSHOT"
+    version = "2.11.10-SNAPSHOT"
 }
 
 #

diff --git a/executorWdl/src/main/resources/application.conf b/executorWdl/src/main/resources/application.conf
@@ -1,5 +1,5 @@
 dxExecutorWdl {
-    version = "2.11.9-SNAPSHOT"
+    version = "2.11.10-SNAPSHOT"
 }
 
 #

diff --git a/scripts/dxcompiler_copy/dxapp.json b/scripts/dxcompiler_copy/dxapp.json
@@ -3,7 +3,7 @@
   "title": "Copy File",
   "summary": "Copy a file to a different region",
   "dxapi": "1.0.0",
-  "version": "0.0.6",
+  "version": "0.0.7",
   "billTo": "org-dnanexus_apps",
   "developers": [
     "org-dnanexus_apps"
@@ -61,14 +61,14 @@
     "azure:westeurope": {
       "systemRequirements": {
         "*": {
-          "instanceType": "azure:mem2_ssd1_v2_x2"
+          "instanceType": "azure:mem1_ssd1_x4"
         }
       }
     },
     "azure:westus": {
       "systemRequirements": {
         "*": {
-          "instanceType": "azure:mem2_ssd1_v2_x2"
+          "instanceType": "azure:mem1_ssd1_x4"
         }
       }
     },
@@ -116,7 +116,7 @@
     }
   },
   "details": {
-    "whatsNew": "* 0.0.6: Added new Bahrain AWS region aws:me-south-1\n * 0.0.5: updated azure instances to v2 for OFH region\n * 0.0.3: Added new London OFH region\n * 0.0.2: Added new London region."
+    "whatsNew": "* 0.0.7: Fixed instance types for Azure regions\n * 0.0.6: Added new Bahrain AWS region aws:me-south-1\n * 0.0.5: updated azure instances to v2 for OFH region\n * 0.0.3: Added new London OFH region\n * 0.0.2: Added new London region."
   },
   "access": {
     "network": [

diff --git a/test/draft2/advanced.wdl b/test/draft2/advanced.wdl
@@ -9,7 +9,7 @@ task BroadGenomicsDocker {
     sed 's/Version: //'
   }
   runtime {
-      docker: "broadinstitute/genomes-in-the-cloud:2.2.4-1469632282"
+      docker: "broadinstitute/genomes-in-the-cloud:2.2.5-1485277291"
       memory: "3 GB"
       cpu: "1"
       disks: "local-disk 10 HDD"

diff --git a/test/draft2/advanced_results.json b/test/draft2/advanced_results.json
@@ -2,5 +2,5 @@
   "advanced.cgrep_count": [8, 0, 3],
   "advanced.str_animals_result" : "Arctic fox_family --K -S --flags --contamination 0 --s foobar",
   "advanced.str_animals_family" : "Family Arctic fox_family",
-  "advanced.BroadGenomicsDocker_version" : "0.7.13-r1126"
+  "advanced.BroadGenomicsDocker_version" : "0.7.15-r1140"
 }
diff --git a/test/draft2/bad_status.wdl b/test/draft2/bad_status.wdl
@@ -3,7 +3,7 @@ task BadCommand {
           ls /xx/yyy
       }
       runtime {
-          docker: "broadinstitute/genomes-in-the-cloud:2.2.4-1469632282"
+          docker: "broadinstitute/genomes-in-the-cloud:2.2.5-1485277291"
       }
       output {
           Int rc = 1