dxpy

DNAnexus toolkit utilities and platform API bindings for Python

Runs as dx|macOS, Linux, Windows|github.com

Command form

ai-draft · 4 tasks · 14 fields

Upload local files to a DNAnexus project and download data objects. All other dx commands (run, describe, build and so on) are not covered.

Opens the form; the finished command lands at your prompt, unrun

Run in Otty

otty gui dxpy

`dx upload`

Upload files

Upload local files or directories to the current DNAnexus project and folder.

Upload filesExample values, fixed in this page — nothing here reaches a terminal

Basic

Local files or directories*

any

Destination path

string

TasksEach one presets the form for one job

Upload files

filenamepath

Upload a directory

filenamerecursivepath

ParametersOnly these flags are editable in the form

Local files or directories

path · positional 0 · repeatable

Destination path

DNAnexus path. A trailing slash means a folder; otherwise it is the final name.
string

--path--destination

Upload directories recursively

boolean

--recursive-r

Create parent folders

boolean

--parents-p

Tag

string · repeatable

--tag

Object type

string · repeatable

--type

Wait until closed

boolean

--wait

No progress bar

boolean

--no-progress

`dx download`

Download data

Download files or folders from DNAnexus to the local machine.

Download dataExample values, fixed in this page — nothing here reaches a terminal

Basic

Objects or folders*

string

Local output

any

TasksEach one presets the form for one job

Download objects

pathoutput

Download a folder

pathrecursiveoutput

ParametersOnly these flags are editable in the form

Objects or folders

Data object IDs or names, or folders.
string · positional 0 · repeatable

Local output

Local filename or directory. Defaults to the object's name on the platform.
path

--output-o

Overwrite local file

Resume an interrupted download if signatures match; otherwise overwrite the local file.
boolean

--overwrite-f

Download folders recursively

boolean

--recursive-r

Download all matches

boolean

--all-a

No progress bar

boolean

--no-progress

SourcesEvery flag above is checked against these

help

usage: dx upload [-h] ... usage: dx download [-h] ...

help2026-10-27

documentation.dnanexus.com

help

usage: dx upload [-h] [--visibility {hidden,visible}] [--property KEY=VALUE] [--type TYPE] [--tag TAG] [--details DETAILS] [-p] [--brief | --verbose] [--env-help] [--path [PATH]] [-r] [--wait] [--no-progress] [--buffer-size WRITE_BUFFER_SIZE] [--singlethread] filename [filen…

help2026-10-27

documentation.dnanexus.com

help

usage: dx download [-h] [--env-help] [-o OUTPUT] [-f] [-r] [-a] [--no-progress] [--lightweight] path [path ...] path Data object ID or name, or folder to download -o, --output OUTPUT Local filename or directory to be used ("-" indicates -f, --overwrite Resume an interupted download if the l…

help2026-10-27

documentation.dnanexus.com

Before it fills your prompt, Otty checks the installed dx against its version. A form that does not match your version is not offered.