From a7a1ac7d2c15ca3d6089eb96e3264c1586d9060a Mon Sep 17 00:00:00 2001 From: Brian Yee Date: Sat, 3 Oct 2026 05:20:26 -0700 Subject: [PATCH 1/2] Add rbp-maps v1.1.0 image Builds the YeoLab/rbp-maps v1.1.0 release tag with Miniforge and the release's own environment.yml (Python 3.13, samtools, bedtools, bedGraphToBigWig, bedToBigBed); publishes ghcr.io/yeolab/rbp-maps:v1.1.0. Co-Authored-By: Claude Opus 5.5 --- CHANGELOG.md | 3 ++ images/rbp-maps/v1.1.0/Dockerfile | 46 +++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 images/rbp-maps/v1.1.0/Dockerfile diff --git a/CHANGELOG.md b/CHANGELOG.md index 880484b..22f03b8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,9 @@ ### Added +- rbp-maps v1.1.0 image (`images/rbp-maps/v1.1.0/Dockerfile`), built from the + upstream release tag with Miniforge and the release's own `environment.yml`; + publishes `ghcr.io/yeolab/rbp-maps:v1.1.0`. - Latest stable containers for the PacBio full-length isoform sequencing note's transcript-visualization and isoform-classification/quantification tools: Swan 3.2, ggtranscript 1.0.0, SQANTI3 6.0.2, TALON 6.0.1, Cerberus diff --git a/images/rbp-maps/v1.1.0/Dockerfile b/images/rbp-maps/v1.1.0/Dockerfile new file mode 100644 index 0000000..21b2eb6 --- /dev/null +++ b/images/rbp-maps/v1.1.0/Dockerfile @@ -0,0 +1,46 @@ +################## BASE IMAGE ###################### + +FROM debian:trixie + +################## METADATA ###################### + +LABEL base_image="debian:trixie" +LABEL version="1" +LABEL software="rbp-maps" +LABEL software.version="v1.1.0" +LABEL about.summary="RNA-binding protein splicing and feature maps from CLIP-seq density or peaks" +LABEL about.url="https://github.com/YeoLab/rbp-maps" +LABEL about.license="MIT" +LABEL about.license_file="" +LABEL about.publication="https://www.ncbi.nlm.nih.gov/pubmed/30413564" +LABEL about.tags="Genomics,Transcriptomics,CLIP-seq,Splicing" + +ARG RBP_MAPS_VERSION=v1.1.0 + +# Builds the tagged release with its own environment.yml (Python 3.13 plus +# samtools, bedtools, bedGraphToBigWig and bedToBigBed from bioconda), using +# Miniforge so only conda-forge/bioconda channels are involved. +RUN apt-get update \ + && apt-get install -y --no-install-recommends \ + ca-certificates \ + curl \ + git \ + procps \ + && rm -rf /var/lib/apt/lists/* \ + && curl -L 'https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh' -o /tmp/miniforge.sh \ + && bash /tmp/miniforge.sh -b -p /opt/conda \ + && rm /tmp/miniforge.sh \ + && git clone --depth 1 --branch "${RBP_MAPS_VERSION}" 'https://github.com/YeoLab/rbp-maps.git' /rbp-maps \ + && /opt/conda/bin/mamba env create -y -p /opt/rbp-maps -f /rbp-maps/environment.yml \ + && /opt/rbp-maps/bin/python -m pip install --no-cache-dir /rbp-maps \ + && /opt/conda/bin/conda clean -afy + +ENV PATH=/opt/rbp-maps/bin:${PATH} +ENV MPLBACKEND=Agg + +# Set defaults for running the image. +# The ENTRYPOINT and CMD are empty to be compatible with +# CWL and WDL implementations that cannot override those values +WORKDIR /rbp-maps +ENTRYPOINT [] +CMD [] From 13f90fa701ffd7ccce40bacd28db6cf941ca7e77 Mon Sep 17 00:00:00 2001 From: Brian Yee Date: Sat, 3 Oct 2026 06:30:23 -0700 Subject: [PATCH 2/2] rbp-maps v1.1.0 image: add JupyterLab for notebook use Lets the image serve the rbp-maps notebook walkthrough through galyleo --sif. A dry run on an identical environment shows only additions (no version changes to the scientific stack). Co-Authored-By: Claude Opus 5.5 --- images/rbp-maps/v1.1.0/Dockerfile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/images/rbp-maps/v1.1.0/Dockerfile b/images/rbp-maps/v1.1.0/Dockerfile index 21b2eb6..d6fa9e3 100644 --- a/images/rbp-maps/v1.1.0/Dockerfile +++ b/images/rbp-maps/v1.1.0/Dockerfile @@ -5,7 +5,7 @@ FROM debian:trixie ################## METADATA ###################### LABEL base_image="debian:trixie" -LABEL version="1" +LABEL version="2" LABEL software="rbp-maps" LABEL software.version="v1.1.0" LABEL about.summary="RNA-binding protein splicing and feature maps from CLIP-seq density or peaks" @@ -19,7 +19,8 @@ ARG RBP_MAPS_VERSION=v1.1.0 # Builds the tagged release with its own environment.yml (Python 3.13 plus # samtools, bedtools, bedGraphToBigWig and bedToBigBed from bioconda), using -# Miniforge so only conda-forge/bioconda channels are involved. +# Miniforge so only conda-forge/bioconda channels are involved. JupyterLab is +# included so the image can serve notebooks (e.g. via galyleo --sif). RUN apt-get update \ && apt-get install -y --no-install-recommends \ ca-certificates \ @@ -33,6 +34,7 @@ RUN apt-get update \ && git clone --depth 1 --branch "${RBP_MAPS_VERSION}" 'https://github.com/YeoLab/rbp-maps.git' /rbp-maps \ && /opt/conda/bin/mamba env create -y -p /opt/rbp-maps -f /rbp-maps/environment.yml \ && /opt/rbp-maps/bin/python -m pip install --no-cache-dir /rbp-maps \ + && /opt/conda/bin/mamba install -y -p /opt/rbp-maps -c conda-forge jupyterlab ipykernel \ && /opt/conda/bin/conda clean -afy ENV PATH=/opt/rbp-maps/bin:${PATH}