Chipenrich

chipenrich/README.md

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+This container is required by the CARLISLE pipeline.

chipenrich/ccbr_chipenrich/Dockerfile.v1

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+FROM bioconductor/bioconductor_docker:RELEASE_3_18
+
+# Set environment variables to reduce interactive prompts during installation
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=Etc/UTC
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    && rm -rf /var/lib/apt/lists/*
+
+LABEL maintainer="Vishal Koparde *(kopardev on GitHub)*"
+LABEL github_handle="kopardev"
+
+# Build time variables
+ARG DOCKERFILE="Dockerfile"
+ENV DOCKERFILE=${DOCKERFILE}
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+ARG IMAGENAME="000000"
+ENV IMAGENAME=${IMAGENAME}
+ARG BASEIMAGENAME="000000"
+ENV BASEIMAGENAME=${BASEIMAGENAME}
+
+# Install Quarto CLI (for HTML report rendering)
+RUN wget -q https://quarto.org/download/latest/quarto-linux-amd64.deb -O /tmp/quarto.deb && \
+    apt-get update && apt-get install -y --no-install-recommends /tmp/quarto.deb && \
+    rm -f /tmp/quarto.deb && rm -rf /var/lib/apt/lists/*
+
+# R/Bioconductor dependencies
+RUN R -q -e "install.packages(c('argparse','tidyverse','viridis'), repos='https://cloud.r-project.org')" && \
+    R -q -e "if (!requireNamespace('BiocManager', quietly=TRUE)) install.packages('BiocManager', repos='https://cloud.r-project.org')" && \
+    R -q -e "BiocManager::install(c('chipenrich','BiocParallel','AnnotationDbi','org.Hs.eg.db','org.Mm.eg.db'), ask=FALSE, update=FALSE)"
+
+# Copy Dockerfile and other files in a single layer
+RUN mkdir -p /opt2 && mkdir -p /data2
+COPY ${DOCKERFILE} /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod -R a+rx /opt2 && chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+WORKDIR /data2
+
+ENTRYPOINT ["/bin/bash"]
+

chipenrich/ccbr_chipenrich/build.sh

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+#!/bin/bash
+REPONAME="ccbr_chipenrich"
+BUILD_TAG="v1"
+docker buildx build \
+  --build-arg REPONAME="${REPONAME}" \
+  --build-arg BUILD_TAG="${BUILD_TAG}" \
+  --build-arg DOCKERFILE="Dockerfile.${BUILD_TAG}" \
+  --build-arg BUILD_DATE=$(date +%Y%m%d) \
+  -t nciccbr/${REPONAME}:${BUILD_TAG} \
+  -f Dockerfile.${BUILD_TAG} \
+  --load .
+

chipenrich/ccbr_chipenrich/push.sh

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+#!/bin/bash
+REPONAME="ccbr_chipenrich"
+BUILD_TAG="v1"
+docker push nciccbr/${REPONAME}:${BUILD_TAG} 
+docker tag nciccbr/${REPONAME}:${BUILD_TAG} nciccbr/${REPONAME}:latest
+docker push nciccbr/${REPONAME}:latest

chipenrich/ccbr_chipenrich/v1-dev.README.md

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+## CCBR/Dockers2 nciccbr/ccbr_chipenrich:v1-dev
+
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/d438907793559cd6aeebedf6d7503c5f3c0609e7/chipenrich/ccbr_chipenrich/Dockerfile.v1
+
+
+Built on: 2026-03-06_22:05:48 
+
+Build tag: v1-dev 
+
+Base image: bioconductor/bioconductor_docker:RELEASE_3_18 
+
+Dockerfile path in repo: chipenrich/ccbr_chipenrich/Dockerfile.v1 
+
+
+| Tool | Version |
+|---------|---------|
+| bcftools | NOTINDOCKER |
+| bedops | NOTINDOCKER |
+| bedtools | NOTINDOCKER |
+| bowtie | NOTINDOCKER |
+| bowtie2 | NOTINDOCKER |
+| bwa | NOTINDOCKER |
+| cutadapt | NOTINDOCKER |
+| git | 2.34.1 |
+| java | 2024-01-16 |
+| multiqc | NOTINDOCKER |
+| parallel | NOTINDOCKER |
+| pigz | NOTINDOCKER |
+| python2 | 2.7.18 |
+| python3 | 3.10.12 |
+| samtools | NOTINDOCKER |
+| vcftools | NOTINDOCKER |