X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/6265dedd0e3d3cdd5696ff87563d2c42ed86f73d..HEAD:/README.md diff --git a/README.md b/README.md index 4ec4bd1cf8..fced2eb5b7 100644 --- a/README.md +++ b/README.md @@ -2,113 +2,95 @@ [comment]: # () [comment]: # (SPDX-License-Identifier: CC-BY-SA-3.0) -# Arvados Workbench 2 +[![Join the chat at https://gitter.im/arvados/community](https://badges.gitter.im/arvados/community.svg)](https://gitter.im/arvados/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) | [Installing Arvados](https://doc.arvados.org/install/index.html) | [Installing Client SDKs](https://doc.arvados.org/sdk/index.html) | [Report a bug](https://dev.arvados.org/projects/arvados/issues/new) | [Development and Contributing](CONTRIBUTING.md) -## Setup -``` -npm install yarn -yarn install -``` + -Install [redux-devtools-extension](https://chrome.google.com/webstore/detail/redux-devtools/lmhkpmbekcpmknklioeibfkpmmfibljd) +[Arvados](https://arvados.org) is an open source platform for +managing, processing, and sharing genomic and other large scientific +and biomedical data. With Arvados, bioinformaticians run and scale +compute-intensive workflows, developers create biomedical +applications, and IT administrators manage large compute and storage +resources. -## Start project for development -``` -yarn start -``` +The key components of Arvados are: -## Start project for development inside Docker container +* *Keep*: Keep is the Arvados storage system for managing and storing large +collections of files. Keep combines content addressing and a +distributed storage architecture resulting in both high reliability +and high throughput. Every file stored in Keep can be accurately +verified every time it is retrieved. Keep supports the creation of +collections as a flexible way to define data sets without having to +re-organize or needlessly copy data. Keep works on a wide range of +underlying filesystems and object stores. -``` -make workbench2-build-image -# (create public/config.json, see "Run time configuration" below) -docker run -ti -v$PWD:$PWD -p 3000:3000 -w$PWD workbench2-build /bin/bash -# (inside docker container) -yarn install -yarn start -``` +* *Crunch*: Crunch is the orchestration system for running [Common Workflow Language](https://www.commonwl.org) workflows. It is +designed to maintain data provenance and workflow +reproducibility. Crunch automatically tracks data inputs and outputs +through Keep and executes workflow processes in Docker containers. In +a cloud environment, Crunch optimizes costs by scaling compute on demand. -## Run unit tests -``` -make unit-tests -``` - -## Run end-to-end tests - -``` -make integration-tests -``` +* *Workbench*: The Workbench web application allows users to interactively access +Arvados functionality. It is especially helpful for querying and +browsing data, visualizing provenance, and tracking the progress of +workflows. -## Run end-to-end tests in a Docker container +* *Command Line tools*: The command line interface (CLI) provides convenient access to Arvados +functionality in the Arvados platform from the command line. -``` -make integration-tests-in-docker -``` +* *API and SDKs*: Arvados is designed to be integrated with existing infrastructure. All +the services in Arvados are accessed through a RESTful API. SDKs are +available for Python, Go, R, Perl, Ruby, and Java. -## Run tests interactively in container +# Quick start -``` -xhost +local:root -ARVADOS_DIR=/path/to/arvados -docker run -ti -v$PWD:$PWD -v$ARVADOS_DIR:/usr/src/arvados -w$PWD --env="DISPLAY" --volume="/tmp/.X11-unix:/tmp/.X11-unix:rw" workbench2-build /bin/bash -(inside container) -yarn run cypress install -tools/run-integration-tests.sh -i -a /usr/src/arvados -``` +To try out Arvados on your local workstation, you can use Arvbox, which +provides Arvados components pre-installed in a Docker container (requires +Docker 1.9+). After cloning the Arvados git repository: -## Production build ``` -yarn build +$ cd arvados/tools/arvbox/bin +$ ./arvbox start localdemo ``` -## Package build -``` -make packages -``` +In this mode you will only be able to connect to Arvbox from the same host. To +configure Arvbox to be accessible over a network and for other options see +http://doc.arvados.org/install/arvbox.html for details. -## Build time configuration -You can customize project global variables using env variables. Default values are placed in the `.env` file. +# Documentation -Example: -``` -REACT_APP_ARVADOS_CONFIG_URL=config.json yarn build -``` +Complete documentation, including the [User Guide](https://doc.arvados.org/user/index.html), [Installation documentation](https://doc.arvados.org/install/index.html), [Administrator documentation](https://doc.arvados.org/admin/index.html) and +[API documentation](https://doc.arvados.org/api/index.html) is available at http://doc.arvados.org/ -## Run time configuration -The app will fetch runtime configuration when starting. By default it will try to fetch `/config.json`. In development mode, this can be found in the `public` directory. -You can customize this url using build time configuration. +If you wish to build the Arvados documentation from a local git clone, see +[doc/README.textile](doc/README.textile) for instructions. -Currently this configuration schema is supported: -``` -{ - "API_HOST": "string", - "FILE_VIEWERS_CONFIG_URL": "string", -} -``` +# Community -### API_HOST +[![Join the chat at https://gitter.im/arvados/community](https://badges.gitter.im/arvados/community.svg)](https://gitter.im/arvados/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) -The Arvados base URL. +The [Arvados community channel](https://gitter.im/arvados/community) +channel at [gitter.im](https://gitter.im) is available for live +discussion and support. -The `REACT_APP_ARVADOS_API_HOST` environment variable can be used to set the default URL if the run time configuration is unreachable. +The [Arvados developement channel](https://gitter.im/arvados/development) +channel at [gitter.im](https://gitter.im) is used to coordinate development. -## FILE_VIEWERS_CONFIG_URL -Local path, or any URL that allows cross-origin requests. See: +The [Arvados user mailing list](http://lists.arvados.org/mailman/listinfo/arvados) +is used to announce new versions and other news. -[File viewers config file example](public/file-viewers-example.json) +All participants are expected to abide by the [Arvados Code of Conduct](CODE_OF_CONDUCT.md). -[File viewers config scheme](src/models/file-viewers-config.ts) +# Reporting bugs -To use the URL defined in the Arvados cluster configuration, remove the entire `FILE_VIEWERS_CONFIG_URL` entry from the runtime configuration. Found in `/config.json` by default. +[Report a bug](https://dev.arvados.org/projects/arvados/issues/new) on [dev.arvados.org](https://dev.arvados.org). -## Plugin support +# Development and Contributing -Workbench supports plugins to add new functionality to the user -interface. For information about installing plugins, the provided -example plugins, see [src/plugins/README.md](src/plugins/README.md). +See [CONTRIBUTING](CONTRIBUTING.md) for information about Arvados development and how to contribute to the Arvados project. +The [development road map](https://dev.arvados.org/issues/gantt?utf8=%E2%9C%93&set_filter=1&gantt=1&f%5B%5D=project_id&op%5Bproject_id%5D=%3D&v%5Bproject_id%5D%5B%5D=49&f%5B%5D=&zoom=1) outlines some of the project priorities over the next twelve months. -## Licensing +# Licensing -Arvados is Free Software. See COPYING for information about Arvados Free -Software licenses. +Arvados is Free Software. See [COPYING](COPYING) for information about the open source licenses used in Arvados.