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Restore missing symlink to python in docker image (SCP-4547) #299

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Merged
merged 1 commit into from
Mar 31, 2023
Merged

Restore missing symlink to python in docker image (SCP-4547) #299

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7 changes: 3 additions & 4 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -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"]
6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion requirements.txt
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Expand Up @@ -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

Expand Down