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Docker update #31

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merged 2 commits into from
Nov 12, 2022
Merged

Docker update #31

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840b599
use htslib 1.16
milkschen Nov 12, 2022
b76e918
update
milkschen Nov 12, 2022
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16 changes: 8 additions & 8 deletions docker/env/Dockerfile
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Expand Up @@ -6,22 +6,22 @@ ENV TZ=America/New_York
ENV VERSION 0.3.0
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
RUN apt-get update && apt-get install -y curl git build-essential cmake libsdsl-dev wget libbz2-dev zlib1g-dev liblzma-dev libncurses-dev zip
RUN wget https://github.com/samtools/htslib/releases/download/1.13/htslib-1.13.tar.bz2 && \
tar -vxjf htslib-1.13.tar.bz2 && \
cd htslib-1.13 && \
RUN wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 && \
tar -vxjf htslib-1.16.tar.bz2 && \
cd htslib-1.16 && \
./configure && \
make && \
make install && \
cd ../ && \
rm htslib-1.13.tar.bz2
RUN wget https://github.com/samtools/samtools/releases/download/1.13/samtools-1.13.tar.bz2 && \
tar -vxjf samtools-1.13.tar.bz2 && \
cd samtools-1.13 && \
rm htslib-1.16.tar.bz2
RUN wget https://github.com/samtools/samtools/releases/download/1.16/samtools-1.16.tar.bz2 && \
tar -vxjf samtools-1.16.tar.bz2 && \
cd samtools-1.16 && \
./configure && \
make && \
make install && \
cd ../ && \
rm samtools-1.13.tar.bz2
rm samtools-1.16.tar.bz2
RUN wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2 && \
tar -vxjf bwa-0.7.17.tar.bz2 && \
cd bwa-0.7.17 && \
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2 changes: 1 addition & 1 deletion docker/production/Dockerfile
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Expand Up @@ -30,7 +30,7 @@ COPY --from=lev /usr/local/bin/meryl /usr/local/bin/
COPY --from=lev /usr/local/bin/samtools /usr/local/bin/
COPY --from=lev /usr/local/lib/libhts.a /usr/local/lib
COPY --from=lev /usr/local/lib/libhts.so /usr/local/lib
COPY --from=lev /usr/local/lib/libhts.so.1.13 /usr/local/lib
COPY --from=lev /usr/local/lib/libhts.so.1.16 /usr/local/lib
COPY --from=lev /usr/local/lib/libhts.so.3 /usr/local/lib
COPY --from=lev /usr/lib/x86_64-linux-gnu/libsdsl.a /usr/local/lib
COPY --from=lev /usr/lib/x86_64-linux-gnu/libsdsl.so /usr/local/lib
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6 changes: 3 additions & 3 deletions docker/update_docker.sh
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Expand Up @@ -15,12 +15,12 @@ docker build --tag leviosam2_env .

# build the production image
cd ../production
docker build --tag leviosam2 .
docker build --tag leviosam2:${VER} --tag leviosam2:latest .

# push using the ${VER} tag
docker tag leviosam2 naechyun/leviosam2:${VER}
# docker tag leviosam2 naechyun/leviosam2:${VER}
docker push naechyun/leviosam2:${VER}

# push using the tag "latest"
docker tag leviosam2 naechyun/leviosam2:latest
# docker tag leviosam2 naechyun/leviosam2:latest
docker push naechyun/leviosam2:latest