diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile index fee230b..b77aa0a 100644 --- a/docker/logan_base/Dockerfile +++ b/docker/logan_base/Dockerfile @@ -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 \ @@ -79,7 +79,7 @@ ENV PATH="/opt2/gatk-4.6.0.0:$PATH" # Picard RUN mkdir picard \ - && wget -O picard/picard.jar https://github.com/broadinstitute/picard/releases/download/3.2.0/picard.jar \ + && wget -O picard/picard.jar https://github.com/broadinstitute/picard/releases/download/3.2.0/picard.jar ENV PICARDJARPATH="/opt2/picard" #Use DISCVRSeq For CombineVariants Replacement @@ -197,9 +197,9 @@ RUN wget https://github.com/AstraZeneca-NGS/VarDictJava/releases/download/v1.8.3 ENV PATH="/opt2/VarDict-1.8.3/bin:$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:$PATH" @@ -233,6 +233,11 @@ RUN wget https://github.com/hartwigmedical/hmftools/releases/download/amber-v4.0 && mv sage_v3.4.4.jar hmftools/sage.jar \ && chmod a+x hmftools/amber.jar ENV PATH="/opt2/hmftools:$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 diff --git a/docker/logan_base/build.sh b/docker/logan_base/build.sh index dd289fb..ea8d8f7 100644 --- a/docker/logan_base/build.sh +++ b/docker/logan_base/build.sh @@ -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 diff --git a/docker/logan_base/meta.yml b/docker/logan_base/meta.yml index 8e76b0a..07bb557 100644 --- a/docker/logan_base/meta.yml +++ b/docker/logan_base/meta.yml @@ -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)"