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README.md

terra-jupyter-bioconductor image

This repo contains the terra-jupyter-bioconductor image that is compatible with notebook service in Terra called Leonardo. For example, use us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:{version} in terra.

Image contents

The terra-jupyter-bioconductor image extends the terra-jupyter-r by including the following:

Bioconductor packages

  • SingleCellExperiment

  • Genomic Features

  • GenomicAlignments

  • ShortRead

  • DESeq2

  • AnnotationHub

  • ExperimentHub

  • ensembldb

  • scRNAseq

  • scran

  • Rtsne

NOTE: The image is able to install all Bioconductor packages as needed by the user. Please use BiocManager::install() to install additional packages.

System dependencies

  • libnetcdf-dev

  • libhdf5-serial-dev

  • libfftw3-dev

  • libopenbabel-dev

  • libopenmpi-dev

  • libexempi3

  • libgdal-dev

  • libcairo2-dev

  • libtiff5-dev

  • libgsl0-dev

  • libgtk2.0-dev

  • libgl1-mesa-dev

  • libglu1-mesa-dev

  • libgmp3-dev

  • libhdf5-dev

  • libncurses-dev

  • libxpm-dev

  • libv8-3.14-dev

  • libgtkmm-2.4-dev

  • libmpfr-dev

  • libudunits2-dev

  • libmodule-build-perl

  • libapparmor-dev

  • libgeos-dev

  • libprotoc-dev

  • librdf0-dev

  • libmagick++-dev

  • libsasl2-dev

  • libpoppler-cpp-dev

  • libprotobuf-dev

  • libpq-dev

  • libperl-dev

  • libarchive-extract-perl

  • libfile-copy-recursive-perl

  • libcgi-pm-perl

  • libdbi-perl

  • libdbd-mysql-perl

  • libxml-simple-perl

  • sqlite

  • openmpi-bin

  • mpi-default-bin

  • openmpi-common

  • openmpi-doc

  • tcl8.5-dev

  • imagemagick

  • tabix

  • ggobi

  • graphviz

  • protobuf-compiler

  • jags

  • xfonts-100dpi

  • xfonts-75dpi

  • biber

  • libsbml

Python packages

  • cwltool

  • pyyaml

  • scikit-learn

  • pandas

To see the complete contents of this image, please see the Dockerfile.

Selecting prior versions of this image

To select older versions of this image, you can search the CHANGELOG.md for a specific version.

Once you find an image version that you want, simply copy and paste the image url from the changelog into the corresponding custom docker field in the Terra notebook runtime widget.

You can’t perform that action at this time.