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15,555 symbols 65,302 edges 2,078 files 2,027 documented · 13%
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README

Join the chat at https://gitter.im/arvados/community | Installing Arvados | Installing Client SDKs | Report a bug | Development and Contributing

Arvados 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.

The key components of Arvados are:

  • 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.

  • Crunch: Crunch is the orchestration system for running Common Workflow Language 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.

  • 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.

  • Command Line tools: The command line interface (CLI) provides convenient access to Arvados functionality in the Arvados platform from the command line.

  • 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.

Documentation

Complete documentation, including the User Guide, Installation documentation, Administrator documentation and API documentation is available at http://doc.arvados.org/

If you wish to build the Arvados documentation from a local git clone, see doc/README.textile for instructions.

Community

Join the chat at https://gitter.im/arvados/community

The Arvados community channel channel at gitter.im is available for live discussion and support.

The Arvados developement channel channel at gitter.im is used to coordinate development.

The Arvados user mailing list is used to announce new versions and other news.

All participants are expected to abide by the Arvados Code of Conduct.

Reporting bugs

Report a bug on dev.arvados.org.

Development and Contributing

See CONTRIBUTING for information about Arvados development and how to contribute to the Arvados project.

The development road map outlines some of the project priorities over the next twelve months.

Licensing

Arvados is Free Software. See COPYING for information about the open source licenses used in Arvados.

Extension points exported contracts — how you extend this code

ExecutorTarget (Interface)
An ExecutorTarget is a remote command execution service. [4 implementers]
lib/cloud/interfaces.go
ContextMenuAction (Interface)
(no doc) [10 implementers]
services/workbench2/src/views-components/context-menu/context-menu-action-set.ts
KeepGateway (Interface)
(no doc) [8 implementers]
sdk/go/arvados/keep_cache.go
APIClient (Interface)
An APIClient performs Arvados API requests. It is typically an *arvados.Client. [3 implementers]
lib/dispatchcloud/container/queue.go
IArvadosClient (Interface)
IArvadosClient is the minimal Arvados API methods used by crunch-run. [3 implementers]
lib/crunchrun/crunchrun.go
TestableVolume (Interface)
A TestableVolume allows test suites to manipulate the state of an underlying Volume, in order to test behavior in cases [3 …
services/keepstore/volume_test.go
ConfigProvider (Interface)
(no doc) [4 implementers]
contrib/java-sdk-v2/src/main/java/org/arvados/client/config/ConfigProvider.java
RoutableFunc (FuncType)
A RoutableFunc calls an API method (sometimes via a wrapped RoutableFunc) that has real argument types. (It is used by
lib/controller/api/routable.go

Core symbols most depended-on inside this repo

Check
called by 4193
services/ws/permission.go
get
called by 2503
services/workbench2/src/services/api/url-builder.ts
dispatch
called by 1702
sdk/python/arvados/commands/arvcli.py
uuid
called by 1348
services/fuse/arvados_fuse/fresh.py
Errorf
called by 759
services/keepstore/volume_generic_test.go
join
called by 528
sdk/cwl/arvados_cwl/fsaccess.py
get
called by 457
sdk/python/arvados/config.py
execute
called by 456
services/workbench2/src/views-components/context-menu/context-menu-action-set.ts

Shape

Method 9,166
Function 3,334
Class 1,454
Struct 754
Interface 574
Route 107
Enum 99
TypeAlias 44
FuncType 23

Languages

Go34%
TypeScript24%
Python22%
Ruby16%
Java4%

Modules by API surface

sdk/python/tests/test_keep_client.py182 symbols
sdk/python/tests/test_arv_put.py139 symbols
services/fuse/tests/test_mount.py134 symbols
sdk/python/tests/test_collections.py127 symbols
sdk/python/arvados/arvfile.py122 symbols
lib/crunchrun/crunchrun_test.go121 symbols
services/fuse/arvados_fuse/fusedir.py114 symbols
sdk/ruby/test/test_collection.rb112 symbols
sdk/go/arvados/fs_collection.go104 symbols
sdk/go/arvados/api.go104 symbols
services/workbench2/src/components/icon/icon.tsx103 symbols
sdk/python/arvados/collection.py103 symbols

For agents

$ claude mcp add arvados \
  -- python -m otcore.mcp_server <graph>

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