dockerfile

FROM python:3.9-slim-buster

RUN groupadd -r sumstats-service && useradd -r --create-home -g sumstats-service sumstats-service

ENV INSTALL_PATH /sumstats_service
RUN mkdir -p $INSTALL_PATH
WORKDIR $INSTALL_PATH

COPY requirements.txt requirements.txt
RUN apt-get update \
    && apt-get install -y --no-install-recommends gcc openssh-client python-dev libmagic-dev \
    && rm -rf /var/lib/apt/lists/* \
    && pip install --upgrade pip \
    && pip install -r requirements.txt \
    && apt-get purge -y --auto-remove gcc python-dev
# the --no-install-recommends helps limit some of the install so that you can be more explicit about what gets installed

COPY . .

RUN pip install -e .

# Expose port:
EXPOSE 8000

RUN mkdir -p logs
RUN chown -R sumstats-service:sumstats-service $INSTALL_PATH

ENV CELERY_PROTOCOL "amqp"
ENV CELERY_USER "guest"
ENV CELERY_PASSWORD "guest"
ENV QUEUE_HOST "rabbitmq.rabbitmq"
ENV QUEUE_PORT 5672
ENV CELERY_QUEUE1 "preval"
ENV CELERY_QUEUE2 "postval"
ENV STORAGE_PATH "./data"
ENV STAGING_PATH "./staging"
ENV DEPO_PATH "./depo_data"
ENV VALIDATED_PATH "./depo_ss_validated"
ENV SW_PATH "./bin"
ENV VALIDATE_WITH_SSH ""
ENV COMPUTE_FARM_LOGIN_NODE ""
ENV COMPUTE_FARM_USERNAME ""
ENV COMPUTE_FARM_QUEUE_LONG ""
ENV SINGULARITY_IMAGE "ebispot/gwas-sumstats-service"
ENV SINGULARITY_TAG "latest"
ENV SINGULARITY_CACHEDIR ""
ENV REMOTE_HTTP_PROXY ""
ENV REMOTE_HTTPS_PROXY ""
ENV GWAS_ENDPOINT_ID ""
ENV CLIENT_SECRET ""
ENV TRANSFER_CLIENT_ID ""
ENV GWAS_GLOBUS_GROUP ""
ENV CLIENT_ID ""
ENV GLOBUS_HOSTNAME ""
ENV MAPPED_COLLECTION_ID ""
ENV STORAGE_GATEWAY_ID ""
ENV FTP_SERVER ""
ENV FTP_USERNAME ""
ENV FTP_PASSWORD ""
ENV MONGO_URI ""
ENV MONGO_USER ""
ENV MONGO_PASSWORD ""
ENV MONGO_DB ""
ENV HTTP_PROXY ""
ENV HTTPS_PROXY ""
ENV no_proxy "localhost,.cluster.local"
ENV DEPO_API_AUTH_TOKEN ""
ENV OUTPUT_PATH "metadata/output"
ENV SUMSTATS_FILE_TYPE ""
ENV GWAS_DEPO_REST_API_URL ""

USER sumstats-service