diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile index e80ed91..d11804b 100644 --- a/docker/logan_base/Dockerfile +++ b/docker/logan_base/Dockerfile @@ -1,4 +1,4 @@ -FROM --platform=linux/amd64 nciccbr/ccbr_ubuntu_base_20.04:v5 +FROM --platform=linux/amd64 nciccbr/ccbr_ubuntu_base_20.04:v6 # build time variables ARG BUILD_DATE="000000" @@ -21,7 +21,7 @@ RUN apt-get update \ && apt-get -y upgrade \ && DEBIAN_FRONTEND=noninteractive apt-get install -y \ bc \ - openjdk-17-jdk + openjdk-17-jdk #Needed for GATK >4 # Common bioinformatics tools # bwa/0.7.17-4 bowtie/1.2.3 bowtie2/2.3.5.1 @@ -48,11 +48,11 @@ RUN wget https://github.com/biod/sambamba/releases/download/v0.8.1/sambamba-0.8. # Install GATK4 (GATK/4.5.0.0) # Requires Java17 -RUN wget https://github.com/broadinstitute/gatk/releases/download/4.5.0.0/gatk-4.5.0.0.zip \ - && unzip /opt2/gatk-4.5.0.0.zip \ - && rm /opt2/gatk-4.5.0.0.zip \ - && /opt2/gatk-4.5.0.0/gatk --list -ENV PATH="/opt2/gatk-4.5.0.0:$PATH" +RUN wget https://github.com/broadinstitute/gatk/releases/download/4.6.0.0/gatk-4.6.0.0.zip \ + && unzip /opt2/gatk-4.6.0.0.zip \ + && rm /opt2/gatk-4.6.0.0.zip \ + && /opt2/gatk-4.6.0.0/gatk --list +ENV PATH="/opt2/gatk-4.6.0.0:$PATH" #Use DISCVRSeq For CombineVariants Replacement @@ -96,12 +96,15 @@ RUN Rscript -e 'BiocManager::install(c("rtracklayer"))' # Install Sequenza-Utils/3.0.0 and Sequenza # Requires R, Python, SAMtools, tabix (already satisfied) # https://cran.r-project.org/web/packages/sequenza/vignettes/sequenza.html#getting-started -##Install Old version of IOtools for parallel processing +# Install Old version of IOtools for parallel processing RUN pip3 install --upgrade pip \ && pip3 install sequenza-utils \ && Rscript -e 'remotes::install_github("ShixiangWang/copynumber"); remotes::install_github("cran/sequenza")' \ && Rscript -e 'remotes::install_version("iotools",version="0.3-2")' +##Install cyvcf2 for processing vcfs in python +RUN pip3 install cyvcf2 + # Install Control-FREEC/v11.6 and additional dependencies # Requires R, samtools, bedtools, sambamba (already satisfied) # http://boevalab.inf.ethz.ch/FREEC/tutorial.html#install @@ -114,10 +117,10 @@ ENV PATH="/opt2/FREEC-11.6/src:$PATH" WORKDIR /opt2 -# Install Somalier/v0.2.16 +# Install Somalier/v0.2.19 # download static binary RUN mkdir somalier \ - && wget -O somalier/somalier https://github.com/brentp/somalier/releases/download/v0.2.16/somalier \ + && wget -O somalier/somalier https://github.com/brentp/somalier/releases/download/v0.2.19/somalier \ && chmod a+rx /opt2/somalier/somalier ENV PATH="/opt2/somalier:$PATH" @@ -189,31 +192,26 @@ RUN wget -O svaba_1.2.0 https://github.com/walaj/svaba/releases/download/v1.2.0/ && mkdir svaba \ && mv svaba_1.2.0 svaba/svaba \ && chmod a+x svaba/svaba - ENV PATH="/opt2/svaba:$PATH" -# MUSE -RUN wget -O muse_2.0.4.tar.gz https://github.com/wwylab/MuSE/archive/refs/tags/v2.0.4.tar.gz \ - && tar -xzf muse_2.0.4.tar.gz \ - && cd MuSE-2.0.4 \ +# MUSE-Use Cloned Version due to -ldeflate option needed +RUN git clone https://github.com/dnousome/MuSE \ + && cd MuSE \ && ./install_muse.sh \ - && mv MuSE /opt2/ \ - && chmod a+x /opt2/MuSE \ - && rm -R /opt2/MuSE-2.0.4 \ - && rm /opt2/muse_2.0.4.tar.gz - + && chmod a+rX /opt2/MuSE/MuSE ENV PATH="/opt2/MuSE:$PATH" +WORKDIR /opt2 # HMFtools for PURPLE/COBALT/AMBER -RUN wget https://github.com/hartwigmedical/hmftools/releases/download/amber-v4.0/amber_v4.0.jar \ +RUN wget https://github.com/hartwigmedical/hmftools/releases/download/amber-v4.0.1/amber_v4.0.1.jar \ && wget https://github.com/hartwigmedical/hmftools/releases/download/cobalt-v1.16/cobalt_v1.16.jar \ && wget https://github.com/hartwigmedical/hmftools/releases/download/purple-v4.0.2/purple_v4.0.2.jar \ - && wget https://github.com/hartwigmedical/hmftools/releases/download/sage-v3.4.3/sage_v3.4.3.jar \ + && wget https://github.com/hartwigmedical/hmftools/releases/download/sage-v3.4.4/sage_v3.4.4.jar \ && mkdir hmftools \ - && mv amber_v4.0.jar hmftools/amber.jar \ + && mv amber_v4.0.1.jar hmftools/amber.jar \ && mv cobalt_v1.16.jar hmftools/cobalt.jar \ && mv purple_v4.0.2.jar hmftools/purple.jar \ - && mv sage_v3.4.3.jar hmftools/sage.jar \ + && mv sage_v3.4.4.jar hmftools/sage.jar \ && chmod a+x hmftools/amber.jar ENV PATH="/opt2/hmftools:$PATH" diff --git a/docker/logan_base/build.sh b/docker/logan_base/build.sh index 5515cc0..90b4446 100644 --- a/docker/logan_base/build.sh +++ b/docker/logan_base/build.sh @@ -5,13 +5,13 @@ #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:v0.3.5 -f Dockerfile . +docker build --platform linux/amd64 --tag ccbr_logan_base:v0.3.6 -f Dockerfile . -docker tag ccbr_logan_base:v0.3.5 dnousome/ccbr_logan_base:v0.3.5 -docker tag ccbr_logan_base:v0.3.5 dnousome/ccbr_logan_base +docker tag ccbr_logan_base:v0.3.6 dnousome/ccbr_logan_base:v0.3.6 +docker tag ccbr_logan_base:v0.3.6 dnousome/ccbr_logan_base -docker push dnousome/ccbr_logan_base:v0.3.5 +docker push dnousome/ccbr_logan_base:v0.3.6 docker push dnousome/ccbr_logan_base:latest