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Dockerfile.cdc
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Dockerfile.cdc
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# build singularity
FROM golang:1.12.5-alpine3.9 as singularity_builder
RUN apk update \
&& apk add --no-cache \
ca-certificates \
build-base \
linux-headers \
git \
openssl-dev \
util-linux-dev \
libseccomp-dev \
gawk \
&& mkdir -p $GOPATH/src/github.com/sylabs \
&& cd $GOPATH/src/github.com/sylabs \
&& git clone -b v3.3.0 https://github.com/sylabs/singularity.git \
&& cd $GOPATH/src/github.com/sylabs/singularity \
&& ./mconfig -s -S -p /opt/singularity \
&& cd $GOPATH/src/github.com/sylabs/singularity/builddir \
&& make \
&& make install
# build final container
FROM alpine:3.9
COPY --from=singularity_builder /opt/singularity /opt/singularity
COPY pipeline.sh /opt/pipeline/
COPY supportFiles/Phila_NC_002942.fna /opt/pipeline/reference/
COPY supportFiles/NC_002942.gff /opt/pipeline/reference/
COPY entrypoint.sh /
# custom certs required for containers to run in CDC network
COPY certs/* /etc/ssl/certs/
RUN apk update \
&& apk add --no-cache \
ca-certificates \
squashfs-tools \
libseccomp \
su-exec \
bash \
&& chmod u+s /opt/singularity/libexec/singularity/bin/starter-suid \
&& chmod -R 755 /opt/pipeline \
&& chmod 644 /etc/ssl/certs/*
ENV PATH /opt/singularity/bin:$PATH
ENTRYPOINT ["/bin/bash", "/entrypoint.sh"]