Commit b19d2b6e authored by Sean Solari's avatar Sean Solari
Browse files

Bug fixes for running docker containers

parent c099310e
......@@ -4,10 +4,26 @@ FROM python:3.8-slim-buster
WORKDIR /app
# Install expam requirements.
RUN apt update
RUN apt-get -y install build-essential
# Install expam.
RUN python3 -m pip install --upgrade pip
RUN python3 -m pip install expam
CMD ["expam", "--help"]
RUN mkdir DATABASE
RUN mkdir INPUT
RUN mkdir OUTPUT
# Download the publicly available expam (test) database.
WORKDIR /app/DATABASE
RUN python3 -m pip install gdown
RUN gdown https://drive.google.com/uc?id=1KRrEvG5Sr28wvkEFW5CXKwcYqLHAu6f7
RUN tar -xvzf test.tar.gz
RUN rm test.tar.gz
RUN rm ._test
# Run database classification.
CMD [ "expam", "classify", "-db", "test", "-d", "/app/INPUT/reads", "-o", "/app/OUTPUT/my_run", "--taxonomy" ]
#!/bin/bash
# Modify source variable to where you would like
# database files to persist on your local computer.
docker run \
--mount type=bind,source=/Users/ssol0002/Documents/Projects/pam/test/data,target=/app/INPUT \
--mount type=bind,source="$(pwd)/OUTPUT",target=/app/OUTPUT \
--shm-size 8G \
-t expam-pip \
\
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