BioContainer (BioFSharp) | BioFSharp

BioContainer Module

Namespace: BioFSharp.BioContainers
Assembly: BioFSharp.BioContainers.dll

BioContainer helper

Types

Type	Description
BcContext
MountInfo

Functions and values

Function or value	Description
`connect str` Full Usage: `connect str` Parameters: str : `string` Returns: `DockerClient`	Connect to docker engine (docker deamon) str : `string` Returns: `DockerClient`
`connectLocalDefault ()` Full Usage: `connectLocalDefault ()` Parameters: () : `unit` Returns: `DockerClient`	Connect to default local docker engine (docker deamon: "npipe://./pipe/docker_engine") () : `unit` Returns: `DockerClient`
`disposeAsync bc` Full Usage: `disposeAsync bc` Parameters: bc : `BcContext` Returns: `Async<unit>`	Disposes the biocontainer context (stops and removes the underlying container) bc : `BcContext` Returns: `Async<unit>`
`execAsync bc cmd` Full Usage: `execAsync bc cmd` Parameters: bc : `BcContext` cmd : `string seq` Returns: `Async<unit>`	Executes a command in the biocontainer context. Passes stdout and stderr of the container to stoud/stderr. bc : `BcContext` cmd : `string seq` Returns: `Async<unit>`
`execReturnAsync bc cmd` Full Usage: `execReturnAsync bc cmd` Parameters: bc : `BcContext` cmd : `string seq` Returns: `Async<string>`	Executes a command in the biocontainer context and returns the either the standard output of the container or the standard error of the container if stdout is empty bc : `BcContext` cmd : `string seq` Returns: `Async<string>`
`getFileAsync bc filePath` Full Usage: `getFileAsync bc filePath` Parameters: bc : `BcContext` filePath : `string` Returns: `Async<Stream>`	Copies file from a container (only single file is supported) bc : `BcContext` filePath : `string` Returns: `Async<Stream>`
`initBcContextAsync connection image` Full Usage: `initBcContextAsync connection image` Parameters: connection : `DockerClient` image : `DockerId` Returns: `Async<BcContext>`	Runs a container of a specified image and keeps it running connection : `DockerClient` image : `DockerId` Returns: `Async<BcContext>`
`initBcContextLocalDefaultAsync image` Full Usage: `initBcContextLocalDefaultAsync image` Parameters: image : `DockerId` Returns: `Async<BcContext>`	Runs a container of a specified image and keeps it running on the local default docker engine image : `DockerId` Returns: `Async<BcContext>`
`initBcContextWithMountAsync connection image hostdirectory` Full Usage: `initBcContextWithMountAsync connection image hostdirectory` Parameters: connection : `DockerClient` image : `DockerId` hostdirectory : `string` Returns: `Async<BcContext>`	Runs a container of a specified image and keeps it running. Bind mounts the host directory under /data/ (without ':' and lower letter according to BioContainer standards). connection : `DockerClient` image : `DockerId` hostdirectory : `string` Returns: `Async<BcContext>`
`putFileAsync bc sourceFileName targetFileName` Full Usage: `putFileAsync bc sourceFileName targetFileName` Parameters: bc : `BcContext` sourceFileName : `string` targetFileName : `string` Returns: `Async<unit>`	Copies file into a container (only single file is supported) bc : `BcContext` sourceFileName : `string` targetFileName : `string` Returns: `Async<unit>`
`putStreamAsync bc sourceStream targetFileName` Full Usage: `putStreamAsync bc sourceStream targetFileName` Parameters: bc : `BcContext` sourceStream : `Stream` targetFileName : `string` Returns: `Async<unit>`	Puts a stream in a container (only single file is supported) bc : `BcContext` sourceStream : `Stream` targetFileName : `string` Returns: `Async<unit>`