diff --git a/Dockerfile b/Dockerfile index 9a9ceaf9..1af023d3 100644 --- a/Dockerfile +++ b/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"] diff --git a/README.md b/README.md index 19284945..667c4a22 100644 --- a/README.md +++ b/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: diff --git a/requirements.txt b/requirements.txt index 2d1c6d17..d6608f52 100644 --- a/requirements.txt +++ b/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