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Revert "[AN-304] Bioconductor 3.20.0 image update" #4812

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Dec 12, 2024
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Revert "[AN-304] Bioconductor 3.20.0 image update" #4812

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8b334a1
Revert "[AN-304] Bioconductor 3.20.0 image update (#4807)"
LizBaldo Dec 11, 2024
18ce7c2
only revert anvil R bioconductor image
LizBaldo Dec 11, 2024
09357f8
update gce and dataproc images
LizBaldo Dec 11, 2024
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8 changes: 4 additions & 4 deletions automation/src/test/resources/reference.conf
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@@ -1,13 +1,13 @@
leonardo {
rImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.6"
rImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-r:2.2.5"
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:2.3.8"
aouImageUrl = "us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.14"
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"
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:3.20.0"
rstudioBioconductorImageUrl = "us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.19.0"
//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-debian11-2024-12-06-04-19-37"
customDataprocImage = "projects/broad-dsp-gcr-public/global/images/leo-dataproc-image-2-1-11-debian11-2024-11-26-16-42-58"

# 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-2024-12-06-03-09-27"
customGceImage = "projects/broad-dsp-gcr-public/global/images/leo-gce-image-2024-08-14-15-03-19"
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:2.2.6"
terra_jupyter_bioconductor="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:2.2.6"
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_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:2.3.8"
terra_jupyter_aou="us.gcr.io/broad-dsp-gcr-public/terra-jupyter-aou:2.2.14"
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"
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:3.20.0"
anvil_rstudio_bioconductor="us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.19.0"

# 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:2.2.6"
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"
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"
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:3.20.0"
anvil_rstudio_bioconductor="us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.19.0"

# 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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