Project Navigation

You can treat dx as an invocation command for navigating the data objects on the DNAnexus Platform. By adding dx in front of commonly used bash commands, you can manage objects on the platform directly from the command-line.

Common commands include:

• dx ls to list objects

• dx cd to change folders

• dx mv to move data objects

• dx cp to copy objects

Listing Objects

Listing Objects in Your Current Project

By default when you set your current project, you are placed in the root folder / of the project. You can list the objects and folders in your current folder with dx ls.

$ dx ls
Developer Quickstart/
Developer Tutorials/
Quickstart/
RNA-seq Workflow Example/
SRR100022/
_README.1st.txt

Listing Object Details

To see more details, you can run the command with the option dx ls -l.

$ dx ls -l
Project: Demo Data (project-BQbJpBj0bvygyQxgQ1800Jkk)
Folder : /
Developer Quickstart/
Developer Tutorials/
Quickstart/
RNA-seq Workflow Example/
SRR100022/
State   Last modified       Size     Name (ID)
closed  2015-09-01 17:55:33 712 bytes _README.1st.txt (file-BgY4VzQ0bvyg22pfZQpXfzgK)

As in bash, you can list the contents of a path.

$ dx ls SRR100022/
SRR100022_1.filt.fastq.gz
SRR100022_2.filt.fastq.gz

Listing Objects in a Different Project

You can also list the contents of a different project. To specify a path that points to a different project, start with the project-ID, followed by a :, then the path within the project where / is the root folder of the project.

Enclose the path in quotes (" ") so dx interprets the spaces as part of the folder name, not as a new command.

$ dx ls "project-BQpp3Y804Y0xbyG4GJPQ01xv:/C. Elegans - Ce10/"
ce10.bt2-index.tar.gz
ce10.bwa-index.tar.gz
ce10.cw2-index.tar.gz
ce10.fasta.fai
ce10.fasta.gz
ce10.tmap-index.tar.gz

Listing Objects That Match a Pattern

You can also list only the objects that match a pattern. In this example, an asterisk * acts as a wildcard to represent all objects with names containing .fasta. This returns only a subset of the objects from the original query.

Enclose the path in quotes for two reasons:

• The shell passes the wildcard pattern to dx without expanding it against local files.

• The dx command correctly interprets any spaces in the path.

$ dx ls "project-BQpp3Y804Y0xbyG4GJPQ01xv:/C. Elegans - Ce10/*.fasta*"
ce10.fasta.fai
ce10.fasta.gz

For more information about using wildcards with dx commands, see Quoting Wildcards in Shell Commands.

Switching Contexts

Changing Folders

To find out your present folder location, use the dx pwd command. You can switch contexts to a subfolder in a project using dx cd.

$ dx pwd
Demo Data:/
$ dx cd Quickstart/
$ dx ls
SRR100022_20_1.fq.gz
SRR100022_20_2.fq.gz

Moving or Renaming Data Objects

You can move and rename data objects and folders using the command dx mv.

To rename an object or a folder, "move" it to a new name in the same folder. Here, a file named ce10.fasta.gz is renamed to C.elegans10.fastq.gz.

$ dx ls
some_folder/
an_applet
ce10.fasta.gz
Variation Calling Workflow
$ dx mv ce10.fasta.gz C.elegans10.fasta.gz
$ dx ls
some_folder/
an_applet
C.elegans10.fasta.gz
Variation Calling Workflow

If you want to move the renamed file into a folder, specify the path to the folder as the destination of the move command (dx mv).

$ dx mv C.elegans10.fasta.gz some_folder/
$ dx ls some_folder/
Hg19
C.elegans10.fasta.gz
...

Copying Objects or Folders to Another Project

You can copy data objects or folders to another project by running the command dx cp. The following example shows how to copy a human reference genome FASTA file (hs37d5.fa.gz) from a public project, "Reference Genome Files", to a project, "Scratch Project", for which the user has ADMINISTER permission.

$ dx select project-BQpp3Y804Y0xbyG4GJPQ01xv
Selected project project-BQpp3Y804Y0xbyG4GJPQ01xv
$ dx cd H.\ Sapiens\ -\ GRCh37\ -\ hs37d5\ (1000\ Genomes\ Phase\ II)/
$ dx ls
hs37d5.2bit
hs37d5.bt2-index.tar.gz
hs37d5.bwa-index.tar.gz
hs37d5.cw2-index.tar.gz
hs37d5.fa.fai
hs37d5.fa.gz
hs37d5.fa.sa
hs37d5.tmap-index.tar.gz
$ dx cp hs37d5.fa.gz project-9z94ZPZvbJ3qP0pyK1P0000p:/
$ dx select project-9z94ZPZvbJ3qP0pyK1P0000p
$ dx ls
some_folder/
an_applet
C.elegans10.fasta.gz
hs37d5.fa.gz
Variation Calling Workflow

You can also copy folders between projects by running dx cp folder_name destination_path. Folders are automatically copied recursively.

The Platform prevents copying a data object within the same project, since each specific data object exists only once in a project. The system also prohibits copying any data object between projects that are located in different cloud regions through dx cp.

Changing Your Current Project

Changing to Another Project With a Project Prompt List

You can change to another project where you want to work by running the command dx select. It displays a prompt with a list of projects for you to select from. In the following example, the user has entered option 2 to select the project named "Mouse".

$ dx select

Note: Use "dx select --level VIEW" or "dx select --public" to select from
projects for which you only have VIEW permission to.

Available projects (CONTRIBUTE or higher):
0) SAM importer test (CONTRIBUTE)
1) Scratch Project (ADMINISTER)
2) Mouse (ADMINISTER)

Project # [1]: 2
Setting current project to: Mouse
$ dx ls -l
Project: Mouse (project-9zVfbG2y8x65kxKY7x20005G)
Folder : /

Changing to a Public Project

To view and select from all public projects, which are available to all DNAnexus users, you can run the command dx select --public:

$ dx select --public

Available public projects:
0) Example 1 (VIEW)
1) Apps Data (VIEW)
2) Parliament (VIEW)
3) CNVkit Tests (VIEW)
...
m) More options not shown...

Pick a numbered choice or "m" for more options: 1

Changing to a Project With VIEW Permission

By default, dx select prompts a list of projects for which you have at least CONTRIBUTE permission. If you want to switch to a project for which you have VIEW permission to view the data objects, you can run dx select --level VIEW to list all the projects in which you have at least VIEW permission.

$ dx select --level VIEW

Available projects (VIEW or higher):
0) SAM importer test (CONTRIBUTE)
1) Scratch Project (ADMINISTER)
2) Shared Applets (VIEW)
3) Mouse (ADMINISTER)

Pick a numbered choice or "m" for more options: 2

Changing Directly to a Specific Project

If you know the project ID or name, you can also give it directly to switch to the project as dx select [project-ID | project-name]:

$ dx select project-9zVfbG2y8x65kxKY7x20005G
Selected project project-9zVfbG2y8x65kxKY7x20005G
$ dx ls -l
Project: Mouse (project-9zVfbG2y8x65kxKY7x20005G)
Folder : /