You can upload files to the DNAnexus platform using the command . You can also upload data using the DNAnexus , a fast and convenient command-line client. For uploading multiple or large files (>50 MB), we recommend that you use Upload Agent, which allows you to upload up to 1000 files concurrently and resume uploads in case of network interruption.
Uploading Files
Uploading One File
You can use the dx upload command followed by a file path to upload one local file.
$ dx upload /Users/alice/README.txt
[===========================================================>] Uploaded 597 of 597 bytes (100%) /Users/alice/README.txt
ID file-xxxx
Class file
Project project-xxxx
Folder /
Name README.txt
State closing
Visibility visible
Types -
Properties -
Tags -
Outgoing links -
Created Sun Jan 1 12:00:01 2017
Created by alice
Last modified Sun Jan 1 12:00:02 2017
archivalState "live"
Media type
You can use the —brief flag with the dx upload command to print only a DNAnexus ID rather than the output shown above. This flag is useful if you want to save the file ID of the uploaded file.
You can also use the dx upload command followed by multiple file paths to upload multiple local files.
$ dx upload /Users/alice/README.txt /Users/bob/README.txt
[===========================================================>] Uploaded 597 of 597 bytes (100%) /Users/alice/README.txt
ID file-xxxx
Class file
Project project-xxxx
Folder /
Name README.txt
State closing
Visibility visible
Types -
Properties -
Tags -
Outgoing links -
Created Sun Jan 1 09:00:01 2017
Created by alice
Last modified Sun Jan 1 09:00:02 2017
archivalState "live"
Media type
[===========================================================>] Uploaded 597 of 597 bytes (100%) /Users/bob/README.txt
ID file-xxxx
Class file
Project project-xxxx
Folder /
Name README.txt
State closing
Visibility visible
Types -
Properties -
Tags -
Outgoing links -
Created Sun Jan 1 09:00:03 2017
Created by alice
Last modified Sun Jan 1 09:00:04 2017
archivalState "live"
Media type
You can use the wildcard * to upload multiple files.
The following command will upload all of the files inside the /Users/alice/ directory. This directory should contain only files and not sub-directories.
$ dx upload /Users/alice/*
[===========================================================>] Uploaded 597 of 597 bytes (100%) /Users/alice/INSTALL.txt
ID file-xxxx
Class file
Project project-xxxx
Folder /
Name INSTALL.txt
State closing
Visibility visible
Types -
Properties -
Tags -
Outgoing links -
Created Sun Jan 1 09:00:01 2017
Created by alice
Last modified Sun Jan 1 09:00:02 2017
archivalState "live"
Media type
[===========================================================>] Uploaded 597 of 597 bytes (100%) /Users/alice/README.txt
ID file-xxxx
Class file
Project project-xxxx
Folder /
Name README.txt
State closing
Visibility visible
Types -
Properties -
Tags -
Outgoing links -
Created Sun Jan 1 09:00:03 2017
Created by alice
Last modified Sun Jan 1 09:00:04 2017
archivalState "live"
Media type
Uploading Directories
You can specify the ‑r/‑‑recursive parameter with the dx upload command to recursively upload one or more directories or folders and maintain their respective structures.
$ dx ls
Users/
$ dx ls Users
alice/
bob/
$ dx ls Users/alice
INSTALL.txt
README.txt
NOTE: If the local uploaded directory ends with the / character, only the contents of the directory will be uploaded, not the directory itself.
Uploading Files With Metadata
If multiple files are uploaded, tags and properties are applied to all of the files.
Properties
You can use the --property KEY=VALUE parameter to add metadata to the file being uploaded. The parameter may be repeated as necessary, e.g. --property key1=val1 --property key2=val2, to link multiple metadata fields as key-value pairs.
$ dx upload /Users/alice/README.txt --property name=alice
[===========================================================>] Uploaded 597 of 597 bytes (100%) /Users/alice/README.txt
ID file-xxxx
Class file
Project project-xxxx
Folder /
Name README.txt
State closing
Visibility visible
Types -
Properties name=alice
Tags -
Outgoing links -
Created Sun Jan 1 09:00:01 2017
Created by alice
Last modified Sun Jan 1 09:00:02 2017
archivalState "live"
Media type
Tags
You can also add tags to uploaded files with the dx upload command using the --tag TAGparameter. The parameter may be repeated as necessary, e.g. --tag tag1 --tag tag2, to link multiple tags to a file.
$ dx upload /Users/alice/README.txt --tag alice
[===========================================================>] Uploaded 597 of 597 bytes (100%) /Users/alice/README.txt
ID file-xxxx
Class file
Project project-xxxx
Folder /
Name README.txt
State closing
Visibility visible
Types -
Properties -
Tags alice
Outgoing links -
Created Sun Jan 1 09:00:01 2017
Created by alice
Last modified Sun Jan 1 09:00:02 2017
archivalState "live"
Media type
Advanced Options
Redirecting Uploaded Files
$ dx upload /Users/alice/README.txt --path /DNAnexus/User/
[===========================================================>] Uploaded 597 of 597 bytes (100%) /Users/alice/README.txt
ID file-xxxx
Class file
Project project-xxxx
Folder /DNAnexus/User
Name README.txt
State closing
Visibility visible
Types -
Properties -
Tags alice
Outgoing links -
Created Sun Jan 1 09:00:01 2017
Created by alice
Last modified Sun Jan 1 09:00:02 2017
archivalState "live"
Media type
Uploading from stdin
You can upload data directly from standard input. This is very useful when streaming the upload while the file is generated.
$ cat /Users/alice/README.txt | dx upload - --path README.txt
ID file-xxxx
Class file
Project project-xxxx
Folder /
Name README.txt
State closing
Visibility visible
Types -
Properties -
Tags alice
Outgoing links -
Created Sun Jan 1 12:00:01 2017
Created by alice
Last modified Sun Jan 1 12:00:02 2017
archivalState "live"
Media type
Buffers
You can specify the --buffer-size parameter with the dx upload command to set the write buffer size in bytes. When uploading large files from standard input, you will need to manually set a --buffer-size because the dx command does not know the file size beforehand.
$ cat /Users/alice/big_file.txt --path big_file.txt | dx upload - --buffer-size 1073741824
ID file-xxxx
Class file
Project project-xxxx
Folder /
Name big_file.txt
State closing
Visibility visible
Types -
Properties -
Tags alice
Outgoing links -
Created Sun Jan 1 12:00:01 2017
Created by alice
Last modified Sun Jan 1 12:05:00 2017
archivalState "live"
Media type
Hiding the Progress Bar
You can specify the --no-progress flag with the dx upload command to hide the progress bar.
$ dx upload /Users/alice/README.txt --no-progress
ID file-xxxx
Class file
Project project-xxxx
Folder /
Name README.txt
State closing
Visibility visible
Types -
Properties -
Tags alice
Outgoing links -
Created Sun Jan 1 12:00:01 2017
Created by alice
Last modified Sun Jan 1 12:00:02 2017
archivalState "live"
Media type
If you are trying to upload a file hosted at a publicly accessible URL rather than locally, you can use the (platform login required to access this link) app.
You can use the command to list the uploaded folders and files.
You can specify object using the dx upload command.
You can use the --path/‑‑destination parameter to specify the DNAnexus destination path. If the path is not specified, dx upload will default to the current project and folder. You can determine your current project and folder using the command .
