Merge pull request #299 from broadinstitute/jlc_fix_image

Restore missing symlink to python in docker image (SCP-4547)

Author: jlchang

Dockerfile

@@ -25,9 +25,8 @@ RUN apt-get -y update && \
 
 RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python3.10
 
-# # Set cleaner defaults (`alias` fails)
-# RUN ln -s /usr/bin/python3.10 /usr/bin/python && \
-#   ln -s /usr/bin/pip3 /usr/bin/pip
+# symlink python3.10 to python
+RUN ln -s /usr/bin/python3.10 /usr/bin/python
 
 # Copy contents of this repo into the Docker image
 # (See .Dockerignore for omitted files)
@@ -36,7 +35,7 @@ COPY . scp-ingest-pipeline
 WORKDIR /scp-ingest-pipeline
 
 # Install Python dependencies
-RUN python3.10 -m pip install -r requirements.txt
+RUN python -m pip install -r requirements.txt
 
 WORKDIR /scp-ingest-pipeline/ingest
 CMD ["python", "ingest_pipeline.py", "--help"]

README.md

@@ -119,10 +119,10 @@ There are some extra steps required, but this sidesteps the need to install pack
 Run the following command to build the testing Docker image locally (make sure Docker is running first). This build command will incorporate any changes in the local instance of your repo, committed or not:
 
 ```
-docker build -t gcr.io/broad-singlecellportal-staging/ingest-pipeline:test-candidate .
+docker build -t ingest-pipeline:test-candidate .
 ```
 
-Note - if this is your first time doing `docker build` you may need to configure Docker to use the Google Cloud CLI to authenticate requests to Container Registry:
+Note - the base Ubuntu image used in the Dockerfile comes from Google Container Registry (GCR, aka gcr.io), if this is your first time doing `docker build` you may need to configure Docker to use the Google Cloud CLI to authenticate requests to Container Registry:
 
 ```
 gcloud auth configure-docker
@@ -163,7 +163,7 @@ Run the container, passing in the proper environment variables:
 docker run --name scp-ingest-test -e MONGODB_USERNAME="$MONGODB_USERNAME" -e DATABASE_NAME="$DATABASE_NAME" \
            -e MONGODB_PASSWORD="$MONGODB_PASSWORD" -e DATABASE_HOST="$DATABASE_HOST" \
            -e GOOGLE_APPLICATION_CREDENTIALS=/tmp/keyfile.json --rm -it \
-           gcr.io/broad-singlecellportal-staging/ingest-pipeline:test-candidate bash
+           ingest-pipeline:test-candidate bash
 ```
 
 Note: on an M1 machine, you may see this message:

requirements.txt

@@ -10,7 +10,7 @@ pandocfilters==1.4.2
 mypy-extensions==0.4.1
 dataclasses==0.6
 colorama==0.4.1
-pymongo==3.9.0
+pymongo==3.12.0
 backoff==1.10.0
 scanpy==1.9.2