{"id":16573255,"url":"https://github.com/jefferis/r-natverse","last_synced_at":"2026-04-20T02:02:32.645Z","repository":{"id":66816506,"uuid":"264369503","full_name":"jefferis/r-natverse","owner":"jefferis","description":"Batteries included docker image for full natverse","archived":false,"fork":false,"pushed_at":"2020-05-17T16:36:58.000Z","size":10,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-01-16T03:33:19.526Z","etag":null,"topics":["docker-image","natverse","neuroanatomy","neuroanatomy-toolbox","neuroscience","r","rstudio"],"latest_commit_sha":null,"homepage":"https://hub.docker.com/r/natverse/r-natverse","language":"Dockerfile","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/jefferis.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-05-16T05:53:25.000Z","updated_at":"2020-05-24T11:52:36.000Z","dependencies_parsed_at":"2023-02-23T14:00:56.381Z","dependency_job_id":null,"html_url":"https://github.com/jefferis/r-natverse","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jefferis%2Fr-natverse","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jefferis%2Fr-natverse/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jefferis%2Fr-natverse/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jefferis%2Fr-natverse/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jefferis","download_url":"https://codeload.github.com/jefferis/r-natverse/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":242048577,"owners_count":20063404,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["docker-image","natverse","neuroanatomy","neuroanatomy-toolbox","neuroscience","r","rstudio"],"created_at":"2024-10-11T21:29:49.207Z","updated_at":"2026-04-20T02:02:27.621Z","avatar_url":"https://github.com/jefferis.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":"# r-natverse\n\n\u003c!-- badges: start --\u003e\n\u003c!-- badges: end --\u003e\n\nThe [natverse](http://natverse.org) is a suite of tools for\nneuroanatomical analysis primarily written in [R](https://www.r-project.org/).\nThe goal of **r-natverse** is to provide a batteries included **natverse**\ninstallation as a single [Docker](https://www.docker.com/) image with all the necessary\ndependencies including R itself and the [RStudio](https://www.rstudio.com/) \ngraphical interface. This is the quickest way to get started with the natverse.\n\n## Quick start\n1. Install [Docker](https://docs.docker.com/get-docker/)\n2. In the terminal \n```\ndocker pull natverse/r-natverse\ndocker run -p 127.0.0.1:8787:8787 \\\n  -e DISABLE_AUTH=true \\\n\t-v \"$HOME\":/home/rstudio \\\n\tnatverse/r-natverse\n```\n3. Open http://127.0.0.1:8787 in your browser!\n4. Find out how to use the **natverse** at http://natverse.org/learn\n\nFor more details about accessing your files and \nuser/security issues read the sections below.\n\n## Introduction \n\nThe *r-natverse* docker image could be useful for\nend users hoping to carry out neuroanatomical analysis or for those\nrunning natverse based services. The base images are provided by\nhttps://hub.docker.com/r/rocker and in particular we are currently\nusing the [tidyverse](https://hub.docker.com/r/rocker/tidyverse)\nseries which are versioned i.e. tied to a particular R version and\nthe state of the MRAN (CRAN snapshot) matching the last date that\nversion was current.\n\nDocker operates on the basis of *images* which can be downloaded and used to run\na *container* on your local machine. The container allows you to run software\nwhich has been installed in a standardised way. Containers typically provide multiple\npieces of software. **r-natverse** provides both R and the RStudio GUI.\n\n## Getting the r-natverse docker image\n\nYou must first have [docker installed](https://docs.docker.com/get-docker/) on your machine.\n\n### Straight from Docker\n\nYou can get the pre-built image straight from Docker:\n\n```\ndocker pull natverse/r-natverse\n```\n\n### Building\n\nYou can also build the container from a local checkout:\n\n```\ngit clone jefferis/r-natverse\ncd r-natverse\nmake\n```\n\n## Run\n\nOnce you have the image, you can run a container. There are a range of different\nways to do this, but the key points are whether you will run the basic R command\nline tool or run the full-featured RStudio GUI. You also need to consider whether\nyou would like to link the container to your regular file system (so that you \ncan access your files outside the container). Finally there may be questions\nabout which *user* your docker images \n\nFor more information about users and volumes go to https://www.rocker-project.org.\n\n### RStudio\nIt is normally recommended to run your Rstudio server with a password. You can \ndo this by replacing `\u003cMYPASSWORD\u003e` in the following command. \n```\ndocker run -e PASSWORD=\"\u003cMYPASSWORD\u003e\" -p 8787:8787 \\\n\t-v \"$HOME\":/home/rstudio \\\n\tnatverse/r-natverse\n```\n\nYou could also set a password via an environment variable. See \nhttps://www.rocker-project.org/use/managing_users/ for more details of users/\nsecurity.\n\nThe -v option links the docker container to your local file system. In \nparticular on most systems `$HOME` will point to your home directory. Inside the\ncontainer, the RStudio application will run as the `rstudio` user, so your files\nwill appear at `/home/rstudio`, which should be the starting path in RStudio.\nSee https://www.rocker-project.org/use/shared_volumes/ for more details.\n\n### R\n\nYou can run the command line version of base R like so: \n\n```\ndocker run -ti -v \"$HOME\":/home/rstudio \\\n  natverse/r-natverse R\n```\n\n## Pros and Cons\n\n### Advantages\n\n* Pre-built Docker image saves installation time - one step install for R, \n  Rsudio and all natverse packages and their dependencies.\n* Avoid installation issues dues to stable container environment\n* Reproducible Research - provides a snapshot of a complete analysis environment.\n  You can use this as a starting point for your own projects and share the full\n  environment with your colleagues.\n\n### Limitations\n\nThe main limitations of using the containerised natverse distribution\n\n* interactive 3D display: support for the the RGL package is not available by \n  default. There is a fall-back to the WebGL plotly 3D graphics but this still \n  has some limitations. See [here](http://natverse.org/nat/articles/plotly.html) \n  for details.\n* speed: performance of Docker containers is surprisingly good in my \n  experience (some benchmarks can even be better than the host system).\n  However there may be limitations in how much memory can be addressed or the\n  number of cores available for parallel processing.\n* Docker may not run on some older systems\n\n## Acknowledgements\n\nBig thanks to the [rocker](https://www.rocker-project.org/) and \n[natverse](http://natverse.org/author/) teams!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjefferis%2Fr-natverse","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjefferis%2Fr-natverse","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjefferis%2Fr-natverse/lists"}