add to publishing steps

Author: lucymcnatt

.github/workflows/publish.yml

@@ -7,6 +7,7 @@ on:
         required: true
         type: choice
         options:
+          - terra-base
           - terra-jupyter-aou
           - terra-jupyter-base
           - terra-jupyter-bioconductor

README.md

@@ -21,7 +21,7 @@ Make sure to go through the [contributing guide](https://github.com/DataBiospher
 Custom docker images need to use a Terra base image (see above) in order to work with the service that runs notebooks on Terra.
 * You can use any of the base images above
   * `terra-base` is the smallest image, but doesn't include any scientific packages on top of Jupyter and R
-* Here is an example of how to build off of a base image: Add `FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:0.0.1` to your dockerfile (`terra-jupyter-base` is the smallest image you can extend from)
+* Here is an example of how to build off of a base image: Add `FROM us.gcr.io/broad-dsp-gcr-public/terra-base:0.0.1` to your dockerfile
 * Customize your image (see the [terra-jupyter-python](terra-jupyter-python/Dockerfile) dockerfile for an example of how to extend from one of our base images
 * Publish the image to either GAR or Dockerhub;
   * If using Dockerhub, the image **must be public** to be used
@@ -88,11 +88,11 @@ Detailed documentation on how to integrate the terra-docker image with Leonardo
 Build the image:
 run `docker build [your_dir] -t [name]`.
 
-`docker build terra-jupyter-base -t terra-jupyter-base`
+`docker build terra-base -t terra-base`
 
 If you're on an M1 and building an image from a locally built image, replace the current FROM command:
 
-`FROM --platform=linux/amd64 terra-jupyter-base`
+`FROM --platform=linux/amd64 terra-base`
 
 Apple Silicon chips later then M1 (ex. M3) need:
 

build_all.sh

@@ -4,15 +4,16 @@
 
 # Create the ordered list of images to build
 # 1- terra-jupyter-base
-# 2- terra-jupyter-python
-# 3- terra-jupyter-r
-# 4- terra-jupyter-gatk
-# 5- terra-jupyter-hail
-# 6- terra-jupyter-aou
-# 7- terra-jupyter-bioconductor
-# 8- terra-rstudio-aou
-# 9- wondershaper
-images=("terra-jupyter-base" "terra-jupyter-python" "terra-jupyter-r" "terra-jupyter-gatk" "terra-jupyter-hail" "terra-jupyter-aou" "terra-jupyter-bioconductor" "terra-rstudio-aou" "wondershaper")
+# 2- terra-jupyter-base
+# 3- terra-jupyter-python
+# 4- terra-jupyter-r
+# 5- terra-jupyter-gatk
+# 6- terra-jupyter-hail
+# 7- terra-jupyter-aou
+# 8- terra-jupyter-bioconductor
+# 9- terra-rstudio-aou
+# 10- wondershaper
+images=("terra-base", "terra-jupyter-base" "terra-jupyter-python" "terra-jupyter-r" "terra-jupyter-gatk" "terra-jupyter-hail" "terra-jupyter-aou" "terra-jupyter-bioconductor" "terra-rstudio-aou" "wondershaper")
 
 # Loop over each image to build in the correct order
 for image in "${images[@]}"; do

config/conf.json

@@ -95,6 +95,24 @@
                 "include_in_custom_gce" : true
             }
         },
+        {
+            "name" : "terra-base",
+            "base_label" : "New Base",
+            "tools" : [
+                "python"
+            ],
+            "packages" : {
+
+            },
+            "version" : "0.0.1",
+            "automated_flags" : {
+                "generate_docs" : true,
+                "include_in_ui" : true,
+                "build" : true,
+                "include_in_custom_dataproc" : true,
+                "include_in_custom_gce" : true
+            }
+        },
         {
             "name" : "terra-jupyter-r",
             "base_label" : "R",

terra-base/CHANGELOG.md

@@ -0,0 +1,10 @@
+## 0.0.1 - 12/16/2025
+
+- Extends GPU-enabled Ubuntu base image
+- Uses Python 3.10
+- Add UV
+- Add conda
+- Add Jupyter
+- Add Leonardo customizations/extensions
+
+Image URL: `us.gcr.io/broad-dsp-gcr-public/terra-base:0.0.1`

terra-base/Dockerfile

@@ -203,7 +203,7 @@ RUN $JUPYTER_HOME/bin/jupyter kernelspec remove python3 -y
 # # Terra-specific Utilities
 # ####################### \
 
-]# Copy over utility scripts and config files
+# Copy over utility scripts and config files
 ENV JUPYTER_SCRIPTS $JUPYTER_HOME/scripts
 ENV JUPYTER_CUSTOM $JUPYTER_HOME/custom
 ENV JUPYTER_EXTENSIONS $JUPYTER_SCRIPTS/extension
@@ -238,6 +238,10 @@ ENV WELDER_USER welder-user
 ENV WELDER_UID 1001
 RUN useradd -m -s /bin/bash -N -u $WELDER_UID $WELDER_USER
 
+# Add an empty file to indicate that this is a terra-base image with a separate jupyer server environment
+# Need a flag to check in the startup scripts to know whether to use the conda environment jupyter
+RUN touch /etc/jupyter/.terra-base-marker
+
 # Make sure that the jupyter user will have access to the jupyter path in the working directory
 EXPOSE $JUPYTER_PORT
 WORKDIR $USER_HOME

terra-base/README.md

@@ -43,12 +43,12 @@ To build the image locally, run the following command in the root of the repo:
 ```
 
 ## NOTE:  Changing paths
-If you change the following paths for the:
+If you change the following paths:
 - `JUPYTER_HOME`
 - `JUPYTER_USER`
 - `CONDA_HOME` 
 
-You may need to update the following files appropriately:
+You may need to update the following files appropriately here and in Leonardo:
 - terra-docker
   - `conda_init.txt`
   - `run_jupyter.sh`