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feat: update docker base
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dnousome committed Jan 2, 2025
1 parent 3edf8aa commit 55d5915
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Showing 3 changed files with 17 additions and 18 deletions.
13 changes: 9 additions & 4 deletions docker/logan_base/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ RUN wget https://github.com/biod/sambamba/releases/download/v0.8.1/sambamba-0.8.
&& mv /opt2/sambamba-0.8.1-linux-amd64-static /opt2/sambamba \
&& chmod a+rx /opt2/sambamba

# Install GATK4 (GATK/4.5.0.0)
# Install GATK4 (GATK/4.6.0.0)
# Requires Java17
RUN wget https://github.com/broadinstitute/gatk/releases/download/4.6.0.0/gatk-4.6.0.0.zip \
&& unzip /opt2/gatk-4.6.0.0.zip \
Expand All @@ -79,7 +79,7 @@ ENV PATH="/opt2/gatk-4.6.0.0:$PATH"

# Picard
RUN mkdir picard \
&& wget -O picard/picard.jar https://github.com/broadinstitute/picard/releases/download/3.2.0/picard.jar \
&& wget -O picard/picard.jar https://github.com/broadinstitute/picard/releases/download/3.2.0/picard.jar
ENV PICARDJARPATH="/opt2/picard"

#Use DISCVRSeq For CombineVariants Replacement
Expand Down Expand Up @@ -197,9 +197,9 @@ RUN wget https://github.com/AstraZeneca-NGS/VarDictJava/releases/download/v1.8.3
ENV PATH="/opt2/VarDict-1.8.3/bin:$PATH"

# Fastp From Opengene github
RUN wget http://opengene.org/fastp/fastp.0.23.4 \
RUN wget http://opengene.org/fastp/fastp.0.24.0 \
&& mkdir fastp \
&& mv fastp.0.23.4 fastp/fastp \
&& mv fastp.0.24.0 fastp/fastp \
&& chmod a+x fastp/fastp
ENV PATH="/opt2/fastp:$PATH"

Expand Down Expand Up @@ -233,6 +233,11 @@ RUN wget https://github.com/hartwigmedical/hmftools/releases/download/amber-v4.0
&& mv sage_v3.4.4.jar hmftools/sage.jar \
&& chmod a+x hmftools/amber.jar
ENV PATH="/opt2/hmftools:$PATH"
WORKDIR /opt2

#GLNEXUS
RUN wget https://github.com/dnanexus-rnd/GLnexus/releases/download/v1.4.1/glnexus_cli \
&& chmod +x glnexus_cli

# Add Dockerfile and argparse.bash script
# and export environment variables
Expand Down
20 changes: 7 additions & 13 deletions docker/logan_base/build.sh
Original file line number Diff line number Diff line change
Expand Up @@ -5,21 +5,15 @@
#docker buildx inspect upbeat_ganguly
#docker buildx build --platform linux/amd64 -f Dockerfile -t dnousome/ccbr_logan_base:v0.3.0 -t dnousome/ccbr_logan_base:latest --push .

docker build --platform linux/amd64 --tag ccbr_logan_base:v0.3.7 -f Dockerfile .
docker build --platform linux/amd64 --tag ccbr_logan_base:v0.3.8 -f Dockerfile .

docker tag ccbr_logan_base:v0.3.7 dnousome/ccbr_logan_base:v0.3.7
docker tag ccbr_logan_base:v0.3.7 dnousome/ccbr_logan_base:latest
docker tag ccbr_logan_base:v0.3.8 dnousome/ccbr_logan_base:v0.3.8
docker tag ccbr_logan_base:v0.3.8 dnousome/ccbr_logan_base:latest


docker push dnousome/ccbr_logan_base:v0.3.7
docker push dnousome/ccbr_logan_base:v0.3.8
docker push dnousome/ccbr_logan_base:latest



# Tag image with version and reset latest
#docker tag ccbr_wgs_base:v0.1.0 nciccbr/ccbr_wgs_base:v0.1.0
#docker tag ccbr_wgs_base:v0.1.0 nciccbr/ccbr_wgs_base

# Push image to DockerHub
#docker push nciccbr/ccbr_wgs_base:v0.1.0
#docker push nciccbr/ccbr_wgs_base:latest
#Pull to CCBR
cd /data/CCBR_Pipeliner/SIFS
singularity pull dnousome-ccbr_logan_base-v0.3.8.img docker://dnousome/ccbr_logan_base:v0.3.8
2 changes: 1 addition & 1 deletion docker/logan_base/meta.yml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
dockerhub_namespace: dnousome
image_name: ccbr_logan_base
version: v0.3.5
version: v0.3.8
container: "$(dockerhub_namespace)/$(image_name):$(version)"

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