Transferring files with Toolchest

Sometimes, there's no alternative to downloading a terabyte of data from an FTP or HTTPS source. When the source download speed is 5 MB/s (looking at you, NCBI RefSeq and EMBL!), the transfer takes days – a long time to keep your laptop up and running.

transfer moves files from any supported input location to any supported output location. It runs in the background, meaning you don't need to keep your laptop or server running during transfer.

Function Call

toolchest.transfer(
    inputs,
    output_path=None,
    is_async=True,
)
toolchest$transfer(
    inputs,
    output_path = NULL,
    is_async = TRUE
)

Function Arguments

Argument

Use in place of:

Description

inputs

input file location

Path to one or more files to be used as input. The files can be a local or remote, see Inputs and Outputs.

output_path

output file location

(optional) Path to a directory to download output files. The path can be local or remote, see see Inputs and Outputs.
If omitted, the transfer isn't completed. The output file is cached on Toolchest infrastructure can be downloaded manually.

is_async

Whether to run the job asynchronously. By default, this is true. If you set this to false, the Toolchest command will wait to exit until the transfer is complete. See Asynchronous Runs for more.


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