From fe499f8be1906b0bc54000bd9417345c5b6c9935 Mon Sep 17 00:00:00 2001 From: EddieLF Date: Fri, 19 Dec 2025 16:31:21 +1100 Subject: [PATCH 1/7] Update mitoreport to v1.2.3 --- images/mitoreport/Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/images/mitoreport/Dockerfile b/images/mitoreport/Dockerfile index 028f83b2..b38c492c 100644 --- a/images/mitoreport/Dockerfile +++ b/images/mitoreport/Dockerfile @@ -1,6 +1,6 @@ FROM ubuntu:22.04 -ARG VERSION=${VERSION:-1.1.0} +ARG VERSION=${VERSION:-1.2.3} LABEL \ version="v${VERSION}" \ @@ -49,8 +49,8 @@ RUN curl -L -O https://github.com/bioinfomethods/mitoreport/releases/download/${ --output resources/mito_map_annotations.json # Requires samtools for local cram > bam -ENV MAMBA_ROOT_PREFIX /root/micromamba -ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH +ENV MAMBA_ROOT_PREFIX="/root/micromamba" +ENV PATH=$MAMBA_ROOT_PREFIX/bin:$PATH RUN wget -qO- https://api.anaconda.org/download/conda-forge/micromamba/0.8.2/linux-64/micromamba-0.8.2-he9b6cbd_0.tar.bz2 | tar -xvj -C /usr/local bin/micromamba && \ mkdir ${MAMBA_ROOT_PREFIX} && \ micromamba install -y --prefix ${MAMBA_ROOT_PREFIX} -c bioconda -c conda-forge \ From b09f2bd8343ad7a1c779d0164c6d1f22a2e6bf33 Mon Sep 17 00:00:00 2001 From: EddieLF Date: Fri, 9 Jan 2026 12:03:51 +1100 Subject: [PATCH 2/7] Remove call to download mito map annotations --- images/mitoreport/Dockerfile | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/images/mitoreport/Dockerfile b/images/mitoreport/Dockerfile index b38c492c..cf85f989 100644 --- a/images/mitoreport/Dockerfile +++ b/images/mitoreport/Dockerfile @@ -44,9 +44,7 @@ WORKDIR /usr/local/bin/ RUN curl -L -O https://github.com/bioinfomethods/mitoreport/releases/download/${VERSION}/mitoreport-${VERSION}-all.jar \ && mv mitoreport-${VERSION}-all.jar mitoreport.jar \ && curl -L -O https://github.com/bioinfomethods/mitoreport/releases/download/${VERSION}/resources.tgz \ - && tar -zxvf resources.tgz \ - && java -jar mitoreport.jar mito-map-download \ - --output resources/mito_map_annotations.json + && tar -zxvf resources.tgz # Requires samtools for local cram > bam ENV MAMBA_ROOT_PREFIX="/root/micromamba" From 7f27b9a4fdfba5335af8a53a2daa82969f7d4f07 Mon Sep 17 00:00:00 2001 From: EddieLF Date: Fri, 9 Jan 2026 12:06:35 +1100 Subject: [PATCH 3/7] Linting --- images/mitoreport/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/images/mitoreport/Dockerfile b/images/mitoreport/Dockerfile index cf85f989..c50cbf17 100644 --- a/images/mitoreport/Dockerfile +++ b/images/mitoreport/Dockerfile @@ -44,7 +44,7 @@ WORKDIR /usr/local/bin/ RUN curl -L -O https://github.com/bioinfomethods/mitoreport/releases/download/${VERSION}/mitoreport-${VERSION}-all.jar \ && mv mitoreport-${VERSION}-all.jar mitoreport.jar \ && curl -L -O https://github.com/bioinfomethods/mitoreport/releases/download/${VERSION}/resources.tgz \ - && tar -zxvf resources.tgz + && tar -zxvf resources.tgz # Requires samtools for local cram > bam ENV MAMBA_ROOT_PREFIX="/root/micromamba" From 78a5f986b2b34e33c6b4de78d939d6ec9f037532 Mon Sep 17 00:00:00 2001 From: EddieLF Date: Fri, 9 Jan 2026 14:48:48 +1100 Subject: [PATCH 4/7] Build Mitoreport from source code and disable file protocol check in main.js --- images/mitoreport/Dockerfile | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/images/mitoreport/Dockerfile b/images/mitoreport/Dockerfile index c50cbf17..aef2f8f8 100644 --- a/images/mitoreport/Dockerfile +++ b/images/mitoreport/Dockerfile @@ -40,11 +40,15 @@ ENV PATH=$PATH:/opt/google-cloud-sdk/bin WORKDIR /usr/local/bin/ -# Install mitoreport and resourses -RUN curl -L -O https://github.com/bioinfomethods/mitoreport/releases/download/${VERSION}/mitoreport-${VERSION}-all.jar \ - && mv mitoreport-${VERSION}-all.jar mitoreport.jar \ - && curl -L -O https://github.com/bioinfomethods/mitoreport/releases/download/${VERSION}/resources.tgz \ - && tar -zxvf resources.tgz +# Instead of downloading JAR, clone and build +# Modify UI to always bypass file:// protocol check (to allow viewing from cloud storage) +RUN git clone https://github.com/bioinfomethods/mitoreport.git /tmp/mitoreport \ + && cd /tmp/mitoreport \ + && git checkout ${VERSION} \ + && sed -i "s/if (window\.location\.protocol === 'file:')/if (true || window.location.protocol === 'file:')/" ui/src/main.js \ + && ./gradlew build \ + && cp build/libs/mitoreport-*-all.jar /usr/local/bin/mitoreport.jar \ + && rm -rf /tmp/mitoreport # Requires samtools for local cram > bam ENV MAMBA_ROOT_PREFIX="/root/micromamba" From 98d1de9154569dbd05a111e0f71bcd7002d40dfe Mon Sep 17 00:00:00 2001 From: EddieLF Date: Fri, 9 Jan 2026 14:56:30 +1100 Subject: [PATCH 5/7] Install git --- images/mitoreport/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/images/mitoreport/Dockerfile b/images/mitoreport/Dockerfile index aef2f8f8..898d5a03 100644 --- a/images/mitoreport/Dockerfile +++ b/images/mitoreport/Dockerfile @@ -18,6 +18,7 @@ RUN apt-get update -y && apt-get install -y --no-install-recommends \ ca-certificates \ curl \ gcc \ + git \ gnupg \ gpg-agent \ libbz2-dev \ From 631a9708232e11113637b725250e9cdf000bca0c Mon Sep 17 00:00:00 2001 From: EddieLF Date: Fri, 9 Jan 2026 15:15:44 +1100 Subject: [PATCH 6/7] Recursive clone, set PROJECT_DIR env var --- images/mitoreport/Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/images/mitoreport/Dockerfile b/images/mitoreport/Dockerfile index 898d5a03..b8d0d9c3 100644 --- a/images/mitoreport/Dockerfile +++ b/images/mitoreport/Dockerfile @@ -38,15 +38,16 @@ RUN curl https://sdk.cloud.google.com > install.sh && \ rm install.sh ENV PATH=$PATH:/opt/google-cloud-sdk/bin +ENV PROJECT_DIR=$(pwd) WORKDIR /usr/local/bin/ # Instead of downloading JAR, clone and build # Modify UI to always bypass file:// protocol check (to allow viewing from cloud storage) -RUN git clone https://github.com/bioinfomethods/mitoreport.git /tmp/mitoreport \ +RUN git clone --recursive https://github.com/bioinfomethods/mitoreport.git /tmp/mitoreport \ && cd /tmp/mitoreport \ && git checkout ${VERSION} \ - && sed -i "s/if (window\.location\.protocol === 'file:')/if (true || window.location.protocol === 'file:')/" ui/src/main.js \ + && sed -i "s/window.location.protocol/true || window.location.protocol/g" ui/src/main.js \ && ./gradlew build \ && cp build/libs/mitoreport-*-all.jar /usr/local/bin/mitoreport.jar \ && rm -rf /tmp/mitoreport From cac32bf640c1ddd6d2b2a5053cbb2b0561cb8087 Mon Sep 17 00:00:00 2001 From: EddieLF Date: Fri, 9 Jan 2026 16:48:59 +1100 Subject: [PATCH 7/7] Revert to v1.1.0, just remove mito map annotation download --- images/mitoreport/Dockerfile | 22 ++++++++-------------- 1 file changed, 8 insertions(+), 14 deletions(-) diff --git a/images/mitoreport/Dockerfile b/images/mitoreport/Dockerfile index b8d0d9c3..49d9c761 100644 --- a/images/mitoreport/Dockerfile +++ b/images/mitoreport/Dockerfile @@ -1,6 +1,6 @@ FROM ubuntu:22.04 -ARG VERSION=${VERSION:-1.2.3} +ARG VERSION=${VERSION:-1.1.0} LABEL \ version="v${VERSION}" \ @@ -18,7 +18,6 @@ RUN apt-get update -y && apt-get install -y --no-install-recommends \ ca-certificates \ curl \ gcc \ - git \ gnupg \ gpg-agent \ libbz2-dev \ @@ -38,23 +37,18 @@ RUN curl https://sdk.cloud.google.com > install.sh && \ rm install.sh ENV PATH=$PATH:/opt/google-cloud-sdk/bin -ENV PROJECT_DIR=$(pwd) WORKDIR /usr/local/bin/ -# Instead of downloading JAR, clone and build -# Modify UI to always bypass file:// protocol check (to allow viewing from cloud storage) -RUN git clone --recursive https://github.com/bioinfomethods/mitoreport.git /tmp/mitoreport \ - && cd /tmp/mitoreport \ - && git checkout ${VERSION} \ - && sed -i "s/window.location.protocol/true || window.location.protocol/g" ui/src/main.js \ - && ./gradlew build \ - && cp build/libs/mitoreport-*-all.jar /usr/local/bin/mitoreport.jar \ - && rm -rf /tmp/mitoreport +# Install mitoreport and resourses +RUN curl -L -O https://github.com/bioinfomethods/mitoreport/releases/download/${VERSION}/mitoreport-${VERSION}-all.jar \ + && mv mitoreport-${VERSION}-all.jar mitoreport.jar \ + && curl -L -O https://github.com/bioinfomethods/mitoreport/releases/download/${VERSION}/resources.tgz \ + && tar -zxvf resources.tgz # Requires samtools for local cram > bam -ENV MAMBA_ROOT_PREFIX="/root/micromamba" -ENV PATH=$MAMBA_ROOT_PREFIX/bin:$PATH +ENV MAMBA_ROOT_PREFIX /root/micromamba +ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH RUN wget -qO- https://api.anaconda.org/download/conda-forge/micromamba/0.8.2/linux-64/micromamba-0.8.2-he9b6cbd_0.tar.bz2 | tar -xvj -C /usr/local bin/micromamba && \ mkdir ${MAMBA_ROOT_PREFIX} && \ micromamba install -y --prefix ${MAMBA_ROOT_PREFIX} -c bioconda -c conda-forge \