diff --git a/CHANGELOG.md b/CHANGELOG.md index ab16555..dcd1f08 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -50,6 +50,9 @@ ### 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`. - Versioned Mandalorion 4.6, ESPRESSO 1.6.0, and Isosceles 0.2.1 containers with build-time installation checks and Singularity pull documentation. - Latest stable containers for the PacBio full-length isoform sequencing diff --git a/images/rbp-maps/v1.1.0/Dockerfile b/images/rbp-maps/v1.1.0/Dockerfile new file mode 100644 index 0000000..d6fa9e3 --- /dev/null +++ b/images/rbp-maps/v1.1.0/Dockerfile @@ -0,0 +1,48 @@ +################## BASE IMAGE ###################### + +FROM debian:trixie + +################## METADATA ###################### + +LABEL base_image="debian:trixie" +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" +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. 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 \ + 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 "${RBP_MAPS_VERSION}" 'https://github.com/YeoLab/rbp-maps.git' /rbp-maps \ + && /opt/conda/bin/mamba env create -y -p /opt/rbp-maps -f /rbp-maps/environment.yml \ + && /opt/rbp-maps/bin/python -m pip install --no-cache-dir /rbp-maps \ + && /opt/conda/bin/mamba install -y -p /opt/rbp-maps -c conda-forge jupyterlab ipykernel \ + && /opt/conda/bin/conda clean -afy + +ENV PATH=/opt/rbp-maps/bin:${PATH} +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 []