├── .gitignore ├── anvil-rstudio-base ├── VERSION ├── rserver.conf ├── CHANGELOG.md ├── Dockerfile └── README.md ├── anvil-rstudio-bioconductor ├── VERSION ├── deps │ └── xvfb_init ├── rserver.conf ├── install.R ├── CHANGELOG.md ├── Dockerfile └── README.md ├── README.md └── LICENSE /.gitignore: -------------------------------------------------------------------------------- 1 | .idea 2 | .DS_Store 3 | -------------------------------------------------------------------------------- /anvil-rstudio-base/VERSION: -------------------------------------------------------------------------------- 1 | 0.0.2 2 | -------------------------------------------------------------------------------- /anvil-rstudio-bioconductor/VERSION: -------------------------------------------------------------------------------- 1 | 0.0.3 2 | -------------------------------------------------------------------------------- /anvil-rstudio-bioconductor/deps/xvfb_init: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | exec /usr/bin/Xvfb :0 -screen 0 800x600x16 3 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # anvil-docker 2 | Docker containers for Anvil Project 3 | 4 | ## AnVIL docker images 5 | 6 | [anvil-rstudio-base](anvil-rstudio-base/) 7 | 8 | [anvil-rstudio-bioconductor](anvil-rstudio-bioconductor/) 9 | -------------------------------------------------------------------------------- /anvil-rstudio-base/rserver.conf: -------------------------------------------------------------------------------- 1 | # Server Configuration File 2 | # See https://support.rstudio.com/hc/en-us/articles/200552316-Configuring-the-Server 3 | 4 | rsession-which-r=/usr/local/bin/R 5 | auth-none=1 6 | www-port=8001 7 | www-address=127.0.0.1 8 | -------------------------------------------------------------------------------- /anvil-rstudio-bioconductor/rserver.conf: -------------------------------------------------------------------------------- 1 | # Server Configuration File 2 | # See https://support.rstudio.com/hc/en-us/articles/200552316-Configuring-the-Server 3 | 4 | rsession-which-r=/usr/local/bin/R 5 | auth-none=1 6 | www-port=8001 7 | www-address=127.0.0.1 8 | -------------------------------------------------------------------------------- /anvil-rstudio-bioconductor/install.R: -------------------------------------------------------------------------------- 1 | # Install Bioconductor packages 2 | BiocManager::install(c( 3 | "SingleCellExperiment", 4 | "GenomicFeatures", 5 | "GenomicAlignments", 6 | "ShortRead", 7 | "DESeq2", 8 | "AnnotationHub", 9 | "ExperimentHub", 10 | "ensembldb", 11 | "scRNAseq", 12 | "scran", 13 | "Rtsne")) 14 | -------------------------------------------------------------------------------- /anvil-rstudio-base/CHANGELOG.md: -------------------------------------------------------------------------------- 1 | 2 | ## 0.0.2 - 11/26/2016 3 | 4 | - Add image tab to rocker/tidyverse:3.6.1 instead of "latest". 5 | - Replace install.packages with BiocManager. 6 | 7 | Image URL: us.gcr.io/anvil-gcr-public/anvil-rstudio-base:0.0.2 8 | 9 | ## 0.0.1 - 10/06/2019 10 | 11 | - Extends rocker/tidyverse image 12 | - Add tidyverse 13 | - Add google-cloud-sdk 14 | - Add googleCloudStorageR 15 | - Add bigrquery 16 | - Add DataBiosphere/Ronaldo 17 | - Add Leonardo customizations 18 | 19 | Image URL: us.gcr.io/anvil-gcr-public/anvil-rstudio-base:0.0.1 20 | -------------------------------------------------------------------------------- /anvil-rstudio-bioconductor/CHANGELOG.md: -------------------------------------------------------------------------------- 1 | ## 0.0.3 - 12/11/2019 2 | 3 | - Pull Bioconductor packages from location on Github. 4 | - This location and set of packages are the same for both RStudio and Jupyter images. 5 | 6 | Image URL: us.gcr.io/anvil-gcr-public/anvil-rstudio-bioconductor:0.0.3 7 | 8 | ## 0.0.2 - 12/10/2019 9 | 10 | - Improve image by adding essential Bioconductor packages. 11 | - Packages list: "AnnotationHub", "ExperimentHub", "ensembldb", "scRNAseq", "scran", "Rtsne" 12 | - Update version of the image to `0.0.2`. 13 | 14 | Image URL: us.gcr.io/anvil-gcr-public/anvil-rstudio-bioconductor:0.0.2 15 | 16 | ## 0.0.1 - 11/26/2019 17 | 18 | - Extends us.gcr.io/anvil-gcr-public/anvil-rstudio-base image. 19 | - Add system dependencies for all bioconductor packages. 20 | 21 | Image URL: us.gcr.io/anvil-gcr-public/anvil-rstudio-bioconductor:0.0.1 22 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2019 AnVIL project 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /anvil-rstudio-base/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM rocker/tidyverse:3.6.1 2 | 3 | # google-cloud-sdk and python dev libs 4 | RUN apt-get update && apt-get install -yq --no-install-recommends \ 5 | gnupg \ 6 | curl \ 7 | lsb-release \ 8 | libpython-dev \ 9 | libpython3-dev \ 10 | && export CLOUD_SDK_REPO="cloud-sdk-$(lsb_release -c -s)" \ 11 | && echo "deb http://packages.cloud.google.com/apt $CLOUD_SDK_REPO main" > /etc/apt/sources.list.d/google-cloud-sdk.list \ 12 | && curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key add - \ 13 | && apt-get update \ 14 | && apt-get install -yq --no-install-recommends \ 15 | google-cloud-sdk \ 16 | && apt-get clean \ 17 | && rm -rf /var/lib/apt/lists/* \ 18 | && curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py \ 19 | && python get-pip.py 20 | 21 | ## TODO: Futureproof the location of the installed packages, make it analogous to the jupyter image and install packages under /home/rstudio/.rpackages 22 | 23 | # google-cloud R packages 24 | RUN R -e "BiocManager::install(c( \ 25 | 'DataBiosphere/Ronaldo', \ 26 | 'bigrquery', \ 27 | 'googleCloudStorageR'))" 28 | 29 | ENV RSTUDIO_PORT 8001 30 | ENV RSTUDIO_HOME /etc/rstudio 31 | 32 | ADD rserver.conf $RSTUDIO_HOME/rserver.conf 33 | 34 | ENV RSTUDIO_USERSETTING /home/rstudio/.rstudio/monitored/user-settings/user-settings 35 | 36 | RUN sed -i 's/alwaysSaveHistory="0"/alwaysSaveHistory="1"/g' $RSTUDIO_USERSETTING \ 37 | && sed -i 's/loadRData="0"/loadRData="1"/g' $RSTUDIO_USERSETTING \ 38 | && sed -i 's/saveAction="0"/saveAction="1"/g' $RSTUDIO_USERSETTING 39 | 40 | EXPOSE $RSTUDIO_PORT 41 | -------------------------------------------------------------------------------- /anvil-rstudio-bioconductor/Dockerfile: -------------------------------------------------------------------------------- 1 | FROM us.gcr.io/anvil-gcr-public/anvil-rstudio-base:0.0.2 2 | 3 | # This is to avoid the error 4 | # 'debconf: unable to initialize frontend: Dialog' 5 | ENV DEBIAN_FRONTEND noninteractive 6 | 7 | # Update apt-get 8 | RUN apt-get update \ 9 | && apt-get install -y --no-install-recommends apt-utils \ 10 | && apt-get install -y dselect \ 11 | && dselect update \ 12 | && apt-get install -y --no-install-recommends \ 13 | pkg-config \ 14 | fortran77-compiler \ 15 | byacc \ 16 | automake \ 17 | ## This section install libraries 18 | libpng-dev \ 19 | libnetcdf-dev \ 20 | libhdf5-serial-dev \ 21 | libfftw3-dev \ 22 | libopenbabel-dev \ 23 | libopenmpi-dev \ 24 | libexempi3 \ 25 | libxt-dev \ 26 | libgdal-dev \ 27 | libjpeg62-turbo-dev \ 28 | libtiff5-dev \ 29 | libreadline-dev \ 30 | libgsl0-dev \ 31 | libgsl2 \ 32 | libgtk2.0-dev \ 33 | libgl1-mesa-dev \ 34 | libglu1-mesa-dev \ 35 | libgmp3-dev \ 36 | libhdf5-dev \ 37 | libncurses-dev \ 38 | libbz2-dev \ 39 | libxpm-dev \ 40 | liblapack-dev \ 41 | libv8-3.14-dev \ 42 | libgtkmm-2.4-dev \ 43 | libmpfr-dev \ 44 | libudunits2-dev \ 45 | libmodule-build-perl \ 46 | libapparmor-dev \ 47 | libgeos-dev \ 48 | libprotoc-dev \ 49 | librdf0-dev \ 50 | libmagick++-dev \ 51 | libpoppler-cpp-dev \ 52 | libprotobuf-dev \ 53 | libperl-dev \ 54 | libz-dev \ 55 | liblzma-dev \ 56 | ## software - perl extentions and modules 57 | libarchive-extract-perl \ 58 | libfile-copy-recursive-perl \ 59 | libcgi-pm-perl \ 60 | libdbi-perl \ 61 | libdbd-mysql-perl \ 62 | libxml-simple-perl \ 63 | ## Databases and other software 64 | sqlite \ 65 | openmpi-bin \ 66 | mpi-default-bin \ 67 | openmpi-common \ 68 | openmpi-doc \ 69 | tcl8.5-dev \ 70 | tk-dev \ 71 | openjdk-8-jdk \ 72 | imagemagick \ 73 | tabix \ 74 | ggobi \ 75 | graphviz \ 76 | protobuf-compiler \ 77 | jags \ 78 | ## Additional resources 79 | xfonts-100dpi \ 80 | xfonts-75dpi \ 81 | biber \ 82 | && apt-get clean \ 83 | && rm -rf /var/lib/apt/lists/* 84 | 85 | ## Python installations 86 | RUN apt-get update \ 87 | && apt-get -y --no-install-recommends install python-dev \ 88 | && pip install wheel \ 89 | ## Install sklearn and pandas on python 90 | && pip install sklearn \ 91 | pandas \ 92 | pyyaml \ 93 | cwltool \ 94 | && apt-get clean \ 95 | && rm -rf /var/lib/apt/lists/* 96 | 97 | # Install libsbml and xvfb 98 | RUN cd /tmp \ 99 | ## libsbml 100 | && curl -O https://s3.amazonaws.com/linux-provisioning/libSBML-5.10.2-core-src.tar.gz \ 101 | && tar zxf libSBML-5.10.2-core-src.tar.gz \ 102 | && cd libsbml-5.10.2 \ 103 | && ./configure --enable-layout \ 104 | && make \ 105 | && make install \ 106 | ## xvfb install 107 | && cd /tmp \ 108 | && curl -SL https://github.com/just-containers/s6-overlay/releases/download/v1.21.8.0/s6-overlay-amd64.tar.gz | tar -xzC / \ 109 | && apt-get update && apt-get install -y --no-install-recommends xvfb \ 110 | && mkdir -p /etc/services.d/xvfb/ \ 111 | ## Clean libsbml, and tar.gz files 112 | && rm -rf /tmp/libsbml-5.10.2 \ 113 | && rm -rf /tmp/libSBML-5.10.2-core-src.tar.gz \ 114 | ## apt-get clean and remove cache 115 | && apt-get clean \ 116 | && rm -rf /var/lib/apt/lists/* 117 | 118 | COPY ./deps/xvfb_init /etc/services.d/xvfb/run 119 | 120 | # Install Bioconductor packages 121 | RUN curl -O https://raw.githubusercontent.com/Bioconductor/anvil-docker/master/anvil-rstudio-bioconductor/install.R \ 122 | && R -f install.R \ 123 | && rm -rf install.R 124 | 125 | USER root 126 | 127 | # Init command for s6-overlay 128 | CMD ["/init"] 129 | -------------------------------------------------------------------------------- /anvil-rstudio-base/README.md: -------------------------------------------------------------------------------- 1 | | Latest Image Release | Docker Image URL | Date Updated | Questions or Feedback | 2 | | --- | --- | --- | --- | 3 | | 0.0.2 | us.gcr.io/anvil-gcr-public/anvil-rstudio-base:0.0.2 | 11/26/2019 | Contact the [Interactive Analysis Team](mailto:workbench-interactive-analysis@broadinstitute.org) | 4 | 5 | # AnVIL RStudio Docker Image 6 | 7 | [Rstudio](https://rstudio.com/products/rstudio/) is an integrated development environment to support the R statistical programming language. The AnVIL RStudio Docker is a version-tagged image of RStudio, providing consistent RStudio software, packages, and dependencies with every use. This document describes the [RStudio](https://rstudio.com/products/rstudio/) Docker Image and how to use it in the cloud-based platform [Terra](app.terra.bio). Unlike the currently existing [Terra base images](https://github.com/DataBiosphere/terra-docker#terra-base-images), RStudio is not hosted in a Jupyter Notebook; any work performed in Terra RStudio will not be saved to a workspace google bucket. This document provides instructions and resources for saving RStudio data and code. 8 | 9 | ## Table of Contents 10 | - [Accessing the AnVIL RStudio Image](#accessing-the-anvil-rstudio-image) 11 | - [Using the RStudio Docker in Terra](#using-the-rstudio-docker-in-terra) 12 | * [Saving RStudio Data](#saving-rstudio-data) 13 | + [1. Copying RStudio work to a workspace google bucket](#1-copying-rstudio-work-to-a-workspace-google-bucket) 14 | + [2. Downloading RStudio files to your local computer](#2-downloading-rstudio-files-to-your-local-computer) 15 | + [3. Checking code into GitHub](#3-checking-code-into-github) 16 | - [RStudio Docker Contents](#rstudio-docker-contents) 17 | * [Base Image](#base-image) 18 | * [Applications](#applications) 19 | * [Libraries](#libraries) 20 | * [Customizations](#customizations) 21 | - [RStudio Docker Updates](#rstudio-docker-updates) 22 | 23 | 24 | ## Accessing the AnVIL RStudio Image 25 | 26 | The AnVIL Rstudio Image can be accessed using the Docker Image URL specified in the table at the top of this document. 27 | 28 | ## Using the RStudio Docker in Terra 29 | 30 | The RStudio Docker can be used in the cloud-based platform Terra. Detailed instructions on accessing the AnVIL RStudio image in Terra can be found in the "[Working with Project-Specific Environments in Terra](https://support.terra.bio/hc/en-us/articles/360037269472)" documentation in Terra support. 31 | 32 | ### Saving RStudio Data 33 | 34 | Unlike in a Terra base Docker image, any work performed in a project-specific Docker (like RStudio) will not be saved to your workspace google bucket. While your code will be saved on the runtime environment, if you delete the runtime (or if your runtime becomes unresponsive), you will lose code. To avoid losing work, make sure to back up your code or save it using the following techniques. 35 | 36 | 37 | #### 1. Copying RStudio work to a workspace google bucket 38 | 39 | Use the [gsutil](https://cloud.google.com/storage/docs/gsutil) tool to copy files to your workspace google bucket. The "[Working with Project-Specific Environments in Terra](https://support.terra.bio/hc/en-us/articles/360037269472)" documentation in Terra support demonstrates how to identify the url for a workspace google bucket. After identifying the workspace google bucket url, you can copy files to a google bucket by navigating to them in your terminal and using the bash command: 40 | 41 | gsutil cp ./* gs:// 42 | 43 | #### 2. Downloading RStudio files to your local computer 44 | Once your files are copied to a workspace google bucket, you can access them by selecting the Data tab of the workspace and choosing the Files option on bottom left. This will display the files available in your google bucket. By selecting a file, you can download it directly. Additionally, [this Terra support document](https://support.terra.bio/hc/en-us/articles/360029251091-Broad-Genomics-Downloading-data-from-a-Terra-workspace) details alternative techniques you can use to download data files. 45 | 46 | #### 3. Checking code into GitHub 47 | You can install Git on RStudio and use it to [check code into GitHub](https://help.github.com/en/github/importing-your-projects-to-github). 48 | 49 | ## RStudio Docker Contents 50 | 51 | ### Base Image 52 | 53 | The base image for the AnVIL RStudio Docker is the [rocker/tidyverse](https://hub.docker.com/r/rocker/tidyverse/) image provided by the [Rocker Project](https://www.rocker-project.org/). This image additionally contains tidyverse and devtools. 54 | 55 | ### Applications 56 | 57 | The AnVIL R Docker contains the [RStudio Server](https://www.rstudio.com/products/rstudio-server/) application which supports a web browser version of RStudio. 58 | 59 | ### Libraries 60 | 61 | The following packages are pre-loaded in the AnVIL RStudio image: 62 | 63 | * [tidyverse](https://www.tidyverse.org/packages/): a suite of packages designed for data sciences 64 | * [google-cloud-sdk](https://cloud.google.com/sdk/): tools for the google cloud platform 65 | * [googleCloudStorageR](http://code.markedmondson.me/googleCloudStorageR/): an R library for interacting with google cloud storage 66 | * [bigrquery](https://github.com/r-dbi/bigrquery): a package to allow interaction with Google's BigQuery 67 | * [DataBiosphere/Ronaldo](https://github.com/DataBiosphere/Ronaldo): a package of functions commonly used for R Notebooks created from Leonardo 68 | 69 | ### Customizations 70 | 71 | The AnVIL RStudio image is customized to disable the RStudio login screen. Future customizations will include: 72 | 73 | * RStudio hooks to refresh credentials 74 | * An RStudio auto pause after inactivity 75 | 76 | ## RStudio Docker Updates 77 | 78 | All updates and changes to the current Docker image are listed in the Rstudio image [CHANGELOG.md file](CHANGELOG.md). 79 | 80 | 81 | 82 | 83 | -------------------------------------------------------------------------------- /anvil-rstudio-bioconductor/README.md: -------------------------------------------------------------------------------- 1 | | Latest Image Release | Docker Image URL |Date Updated | Questions or Feedback | 2 | | --- | --- | --- | --- | 3 | | 0.0.3 | us.gcr.io/anvil-gcr-public/anvil-rstudio-bioconductor:0.0.3 | 12/11/2019 | Contact the [Bioconductor Team](mailto:nitesh.turaga@roswellpark.org) | 4 | 5 | # RStudio-Bioconductor Docker Image 6 | 7 | [Rstudio](https://rstudio.com/products/rstudio/) is an integrated development environment to support the R statistical programming language. The AnVIL RStudio Bioconductor Docker is an RStudio environment that supports [Bioconductor](https://www.bioconductor.org/), an open source software for bioinformatic analyses. The RStudio Bioconductor Docker is based off the AnVIL RStudio Docker, a version-tagged image of RStudio, providing consistent RStudio software, packages, and dependencies with every use. This document describes the RStudio Bioconductor Docker Image and how to use it in the cloud-based platform [Terra](app.terra.bio). Unlike the currently existing [Terra base images](https://github.com/DataBiosphere/terra-docker#terra-base-images), RStudio is not hosted in a Jupyter Notebook; any work performed in Terra RStudio will not be saved to a workspace google bucket. This document provides instructions and resources for saving RStudio data and code. 8 | 9 | ## Table of Contents 10 | - [Accessing the AnVIL RStudio Bioconductor Image](#accessing-the-anvil-rstudio-bioconductor-image) 11 | - [Using RStudio in Terra](#using-rstudio-in-terra) 12 | * [Saving RStudio Data](#saving-rstudio-data) 13 | + [1. Copying RStudio work to a workspace google bucket](#1-copying-rstudio-work-to-a-workspace-google-bucket) 14 | + [2. Downloading RStudio files to your local computer](#2-downloading-rstudio-files-to-your-local-computer) 15 | + [3. Checking code into GitHub](#3-checking-code-into-github) 16 | - [RStudio Bioconductor Docker Contents](#rstudio-bioconductor-docker-contents) 17 | + [Base Image](#base-image) 18 | + [Applications](#applications) 19 | + [Libraries](#libraries) 20 | + [Customizations](#customizations) 21 | + [Dependencies](#dependencies) 22 | - [RStudio Bioconductor Updates](#rstudio-bioconductor-updates) 23 | 24 | 25 | # Accessing the AnVIL RStudio Bioconductor Image 26 | 27 | The AnVIL Rstudio Bioconductor Image can be accessed using the Docker Image URL specified in the table at the top of this document. 28 | 29 | # Using RStudio in Terra 30 | 31 | The RStudio Docker can be used in the cloud-based platform Terra. Detailed instructions on accessing the AnVIL RStudio image in Terra can be found in the "[Working with Project-Specific Environments in Terra](https://support.terra.bio/hc/en-us/articles/360037269472)" documentation in Terra support. 32 | 33 | ## Saving RStudio Data 34 | 35 | Unlike in a Terra base Docker image, any work performed in a project-specific Docker (like RStudio) will not be saved to your workspace google bucket. While your code will be saved on the runtime environment, if you delete the runtime (or if your runtime becomes unresponsive), you will lose code. To avoid losing work, make sure to back up your code or save it using the following techniques. 36 | 37 | ### 1. Copying RStudio work to a workspace google bucket 38 | 39 | Use the [gsutil](https://cloud.google.com/storage/docs/gsutil) tool to copy files to your workspace google bucket. The "[Working with Project-Specific Environments in Terra](https://support.terra.bio/hc/en-us/articles/360037269472)" documentation in Terra support demonstrates how to identify the URL for a workspace google bucket. After identifying the workspace google bucket URL, you can copy files to a google bucket by navigating to them in your terminal and using the bash command: 40 | 41 | gsutil cp ./* gs:// 42 | 43 | ### 2. Downloading RStudio files to your local computer 44 | Once your files are copied to a workspace google bucket, you can access them by selecting the Data tab of the workspace and choosing the Files option on the bottom left. This will display the files available in your google bucket. By selecting a file, you can download it directly. Additionally, [this Terra support document](https://support.terra.bio/hc/en-us/articles/360029251091-Broad-Genomics-Downloading-data-from-a-Terra-workspace) details alternative techniques you can use to download data files. 45 | 46 | ### 3. Checking code into GitHub 47 | You can install Git on RStudio and use it to [check code into GitHub](https://help.github.com/en/github/importing-your-projects-to-github). 48 | 49 | # RStudio Bioconductor Docker Contents 50 | 51 | ### Base Image 52 | 53 | The base image for the AnVIL RStudio Bioconductor Docker is the [RStudio Docker](https://github.com/anvilproject/anvil-docker/tree/master/anvil-rstudio-base). This contains the [rocker/tidyverse](https://hub.docker.com/r/rocker/tidyverse/) image provided by the [Rocker Project](https://www.rocker-project.org/), as well as tidyverse and devtools. 54 | 55 | ### Applications 56 | 57 | The AnVIL RStudio Docker contains the [RStudio Server](https://www.rstudio.com/products/rstudio-server/) application which supports a web browser version of RStudio. Additionally, it contains all system dependencies for Bioconductor packages. 58 | 59 | ### Libraries 60 | The Bioconductor image inherits all libraries from `anvil-rstudio-base`. The following packages are included in the base image: 61 | * [tidyverse](https://www.tidyverse.org/packages/): a suite of packages designed for data sciences 62 | * [google-cloud-sdk](https://cloud.google.com/sdk/): tools for the google cloud platform 63 | * [googleCloudStorageR](http://code.markedmondson.me/googleCloudStorageR/): an R library for interacting with google cloud storage 64 | * [bigrquery](https://github.com/r-dbi/bigrquery): a package to allow interaction with Google's BigQuery 65 | * [DataBiosphere/Ronaldo](https://github.com/DataBiosphere/Ronaldo): a package of functions commonly used for R Notebooks created from Leonardo 66 | 67 | The following are Bioconductor Docker-specific packages: 68 | * [BiocManager](https://www.bioconductor.org/install/): a tool for installing Bioconductor packages 69 | * [SingleCellExperiment](): an S4 container for single-cell analyses 70 | * [GenomicFeatures](https://www.bioconductor.org/packages/release/bioc/html/GenomicFeatures.html): tools for manipulating transcript annotations 71 | * [GenomicAlignments](https://www.bioconductor.org/help/search/index.html?q=GenomicAlignments/): containers for storing short genomic alignments 72 | * [ShortRead](https://www.bioconductor.org/packages/release/bioc/html/ShortRead.html): tools for manipulating and assessing FASTQs 73 | * [DESeq2](https://www.bioconductor.org/help/search/index.html?q=DESeq2/): tools for RNAseq analyses 74 | * [AnnotationHub](https://www.bioconductor.org/packages/release/bioc/html/AnnotationHub.html): resources for gene annotation 75 | * [ExperimentHub](https://www.bioconductor.org/packages/release/bioc/html/ExperimentHub.html): tools for accessing curated experiments 76 | * [ensembldb](https://www.bioconductor.org/packages/release/bioc/html/ensembldb.html): tools for making Ensembl-based annotations 77 | * [scRNAseq](https://www.bioconductor.org/packages/release/data/experiment/html/scRNAseq.html): a collection of public, single-cell RNAseq datasets 78 | * [scran](https://www.bioconductor.org/packages/release/bioc/html/scran.html): tools for single-cell analyses 79 | * [Rtsne](https://cran.r-project.org/web/packages/Rtsne/index.html): an R package for making tSNE plots 80 | 81 | ### Customizations 82 | 83 | The AnVIL RStudio image is customized to disable the RStudio login screen. Future customizations will include: 84 | 85 | * RStudio hooks to refresh credentials 86 | * An RStudio auto pause after inactivity 87 | 88 | ### Dependencies 89 | **System Dependencies** 90 | * fortran77-compiler 91 | * byacc 92 | * automake 93 | * libpng-dev 94 | * libnetcdf-dev 95 | * libhdf5-serial-dev 96 | * libfftw3-dev 97 | * libopenbabel-dev 98 | * libopenmpi-dev 99 | * libexempi3 100 | * libxt-dev 101 | * libgdal-dev 102 | * libjpeg62-turbo-dev 103 | * libtiff5-dev 104 | * libreadline-dev 105 | * libgsl0-dev 106 | * libgsl2 107 | * libgtk2.0-dev 108 | * libgl1-mesa-dev 109 | * libglu1-mesa-dev 110 | * libgmp3-dev 111 | * libhdf5-dev 112 | * libncurses-dev 113 | * libbz2-dev 114 | * libxpm-dev 115 | * liblapack-dev 116 | * libv8-3.14-dev 117 | * libgtkmm-2.4-dev 118 | * libmpfr-dev 119 | * libudunits2-dev 120 | * libmodule-build-perl 121 | * libapparmor-dev 122 | * libgeos-dev 123 | * libprotoc-dev 124 | * librdf0-dev 125 | * libmagick++-dev 126 | * libpoppler-cpp-dev 127 | * libprotobuf-dev 128 | * libperl-dev 129 | * libz-dev 130 | * liblzma-dev 131 | 132 | **Bioconductor Dependencies** 133 | * libsbml 134 | * xvfb 135 | 136 | **Perl Dependencies** 137 | * libarchive-extract-perl 138 | * libfile-copy-recursive-perl 139 | * libcgi-pm-perl 140 | * libdbi-perl 141 | * libdbd-mysql-perl 142 | * libxml-simple-perl 143 | 144 | **Python Dependencies** 145 | * python-dev 146 | * sklearn 147 | * pandas 148 | * pyyaml 149 | * cwltool 150 | 151 | **Additional Dependencies** 152 | * xfonts-100dpi 153 | * xfonts-75dpi 154 | * biber 155 | 156 | **Databases and Other Software** 157 | * sqlite 158 | * openmpi-bin 159 | * mpi-default-bin 160 | * openmpi-common 161 | * openmpi-doc 162 | * tcl8.5-dev 163 | * tk-dev 164 | * openjdk-8-jdk 165 | * imagemagick 166 | * tabix 167 | * ggobi 168 | * graphviz 169 | * protobuf-compiler 170 | * jags 171 | 172 | # RStudio Bioconductor Updates 173 | 174 | All updates and changes to the current RStudio Bioconductor Docker image are listed in the Rstudio image [CHANGELOG.md file](CHANGELOG.md). 175 | 176 | 177 | 178 | --------------------------------------------------------------------------------