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Upgrade Docker to use Python 3.7 (SCP-2056) #70

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Merged
eweitz merged 6 commits into from
Jan 7, 2020
Merged

Upgrade Docker to use Python 3.7 (SCP-2056) #70

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7873761
Upgrade from Python 3.6 to 3.7 in Docker image
eweitz Jan 6, 2020
510f273
Fix default Docker commmand for basic smoke test
eweitz Jan 6, 2020
ced8b36
Debug updated Docker build
eweitz Jan 7, 2020
7485107
Fix symbolic links to specify Python 3.7
eweitz Jan 7, 2020
fad47eb
Use pip from Python 3.7
eweitz Jan 7, 2020
52128a8
Copyedit: Homo Sapiens -> Homo sapiens
eweitz Jan 7, 2020
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20 changes: 10 additions & 10 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -12,19 +12,19 @@
# https://github.com/GoogleContainerTools/base-images-docker/tree/master/ubuntu
FROM marketplace.gcr.io/google/ubuntu1804:latest

#RUN echo "Uncomment to clear cached layers below this statement (20190708-1259)"
# RUN echo "Uncomment to clear cached layers below this statement (2020-01-07-0947)"

# Install Python 3.6
# (Auxiliary Ubuntu packages for Python assume Python 3.6;
# configuring them for Python >= 3.7 is not straightforward.)
# Install Python 3.7
RUN apt-get -y update && \
apt -y install software-properties-common dirmngr apt-transport-https lsb-release ca-certificates && \
apt -y install software-properties-common && \
add-apt-repository ppa:deadsnakes/ppa && \
apt -y install python3.6 && \
apt -y install python3-pip
apt -y install python3-pip && \
apt -y install python3.7

RUN python3.7 -m pip install pip

# Set cleaner defaults (`alias` fails)
RUN ln -s /usr/bin/python3 /usr/bin/python && \
RUN ln -s /usr/bin/python3.7 /usr/bin/python && \
ln -s /usr/bin/pip3 /usr/bin/pip

# Copy contents of this repo into the Docker image
Expand All @@ -34,7 +34,7 @@ COPY . scp-ingest-pipeline
WORKDIR /scp-ingest-pipeline

# Install Python dependencies
RUN pip install -r requirements.txt
RUN python3.7 -m pip install -r requirements.txt

WORKDIR /scp-ingest-pipeline/ingest
CMD ["python", "ingest.py", "--help"]
CMD ["python", "ingest_pipeline.py", "--help"]
2 changes: 1 addition & 1 deletion ingest/ingest_pipeline.py
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Expand Up @@ -31,7 +31,7 @@
python ingest_pipeline.py --study-id 5d276a50421aa9117c982845 --study-file-id 5dd5ae25421aa910a723a337 ingest_subsample --cluster-file ../tests/data/test_1k_cluster_Data.csv --name custer1 --cell-metadata-file ../tests/data/test_1k_metadata_Data.csv --subsample

# Ingest mtx files
python ingest_pipeline.py --study-id 5d276a50421aa9117c982845 --study-file-id 5dd5ae25421aa910a723a337 ingest_expression --taxon-name 'Homo Sapiens' --taxon-common-name humans --matrix-file ../tests/data/matrix.mtx --matrix-file-type mtx --gene-file ../tests/data/genes.tsv --barcode-file ../tests/data/barcodes.tsv
python ingest_pipeline.py --study-id 5d276a50421aa9117c982845 --study-file-id 5dd5ae25421aa910a723a337 ingest_expression --taxon-name 'Homo sapiens' --taxon-common-name humans --matrix-file ../tests/data/matrix.mtx --matrix-file-type mtx --gene-file ../tests/data/genes.tsv --barcode-file ../tests/data/barcodes.tsv
"""
import argparse
from typing import Dict, Generator, List, Tuple, Union # noqa: F401
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