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[AN-304] Bioconductor 3.20.0 image update #4807

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Merged
LizBaldo merged 3 commits into from
Dec 6, 2024
Merged

[AN-304] Bioconductor 3.20.0 image update #4807

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6479741
update latest bioconductor, gatk, and aou images
LizBaldo Dec 6, 2024
40b8d2c
also update images for integration tests
LizBaldo Dec 6, 2024
ae12e8f
point to new dataproc and gce images
LizBaldo Dec 6, 2024
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8 changes: 4 additions & 4 deletions automation/src/test/resources/reference.conf
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
leonardo {
rImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5"
rImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6"
pythonImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.5"
hailImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.1.12"
gatkImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.7"
aouImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.13"
gatkImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.8"
aouImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.14"
baseImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.3"
gcrWelderUri = "us.gcr.io/broad-dsp-gcr-public/welder-server"
dockerHubWelderUri = "broadinstitute/welder-server"
rstudioBioconductorImageUrl = "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.19.0"
rstudioBioconductorImageUrl = "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.20.0"
//each fiab will have a unique topic name sourced from leonardo.conf, this is never published to in automation tests to ensure pub/sub components can auth properly, but never read from to avoid conflicts.
topicName = "leonardo-pubsub-test"
location = "us-central1-a"
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4 changes: 2 additions & 2 deletions http/src/main/resources/reference.conf
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Expand Up @@ -70,7 +70,7 @@ dataproc {
}

# Cached dataproc image used by Terra
customDataprocImage = "projects/broad-dsp-gcr-public/global/images/leo-dataproc-image-2-1-11-debian11-2024-11-26-16-42-58"
customDataprocImage = "projects/broad-dsp-gcr-public/global/images/leo-dataproc-image-2-1-11-debian11-2024-12-06-04-19-37"

# The ratio of memory allocated to spark. 0.8 = 80%.
# Hail/Spark users generally allocate 80% of the ram to the JVM.
Expand Down Expand Up @@ -111,7 +111,7 @@ dataproc {
}

gce {
customGceImage = "projects/broad-dsp-gcr-public/global/images/leo-gce-image-2024-08-14-15-03-19"
customGceImage = "projects/broad-dsp-gcr-public/global/images/leo-gce-image-2024-12-06-03-09-27"
userDiskDeviceName = "user-disk"
defaultScopes = [
"https://www.googleapis.com/auth/userinfo.email",
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10 changes: 5 additions & 5 deletions jenkins/dataproc-custom-images/prepare-custom-leonardo-jupyter-dataproc-image.sh
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Expand Up @@ -17,14 +17,14 @@ set -e -x
#

terra_jupyter_python="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.5"
terra_jupyter_r="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5"
terra_jupyter_bioconductor="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.2.5"
terra_jupyter_r="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6"
terra_jupyter_bioconductor="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.2.6"
terra_jupyter_hail="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-hail:1.1.12"
terra_jupyter_gatk="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.7"
terra_jupyter_aou="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.13"
terra_jupyter_gatk="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.8"
terra_jupyter_aou="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.14"
welder_server="us.gcr.io/broad-dsp-gcr-public/welder-server:8667bfe"
openidc_proxy="broadinstitute/openidc-proxy:2.3.1_2"
anvil_rstudio_bioconductor="us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.19.0"
anvil_rstudio_bioconductor="us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.20.0"

# Note that this is the version used currently by AOU in production, the one above can be staged for testing
terra_jupyter_aou_old="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.13"
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10 changes: 5 additions & 5 deletions jenkins/gce-custom-images/prepare_gce_image.sh
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Expand Up @@ -17,13 +17,13 @@ set -e -x
#

terra_jupyter_python="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-python:1.1.5"
terra_jupyter_r="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5"
terra_jupyter_bioconductor="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.2.5"
terra_jupyter_gatk="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.7"
terra_jupyter_aou="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.13"
terra_jupyter_r="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6"
terra_jupyter_bioconductor="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.2.6"
terra_jupyter_gatk="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-gatk:2.3.8"
terra_jupyter_aou="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.14"
welder_server="us.gcr.io/broad-dsp-gcr-public/welder-server:8667bfe"
openidc_proxy="broadinstitute/openidc-proxy:2.3.1_2"
anvil_rstudio_bioconductor="us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.19.0"
anvil_rstudio_bioconductor="us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.20.0"

# Note that this is the version used currently by AOU in production, the one above can be staged for testing
terra_jupyter_aou_old="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.13"
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