Project Navigation
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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 (e.g. dx ls, dx cd, dx mv, and dx cp), you can list objects, change folders, move data objects, and copy objects stored in the platform; all on the command-line.
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 .
To see more details, you can run the command with the option dx ls -l.
As in bash, you can list the contents on a path.
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.
Note that we enclosed our path with quotes (" "), so dx interprets the spaces as part of the folder name, not as a new command.
You can also list only the objects which match a pattern. Here, we use a * as a wildcard to represent all objects whose names contain .fasta. This returns only a subset of the objects returned in the original query. Again we enclosed our path in " " so dx correctly interprets the asterisk and the spaces in the path.
To rename an object or a folder, simply "move" it to a new name in the same folder. Here we rename a file named ce10.fasta.gz to C.elegans10.fastq.gz.
If we wanted to move the renamed file into a folder, we can specify the path to the folder as the destination of the move command.
You can copy data objects or folders to another project by running the command dx cp. Below we show an example to copy a human reference genome FASTA file (hs37d5.fa.gz) from a public project, “Reference Genome Files”, to a project “Scratch Project” that the user has ADMINISTER permission to.
You can also copy folders between projects by running dx cp folder_name destination_path. Folders will automatically be copied recursively.
To view and select between all public projects, projects available to all DNAnexus users, you can run the command dx select --public:
By default, dx select will prompt list of projects that you have at least CONTRIBUTE permission to. If you wanted to switch to a project that you have VIEW permission to 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 to.
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]:
To find out what folder you are currently in, you can use the dx pwd command. You can switch contexts to a subfolder in a project using .
You can move and rename data objects and folders using the command .
NOTE: The platform does NOT allow copying a data object within the same project, since each specific data object would exist only once in a project. Additionally, it is prohibited to copy any data object between projects that located in different through dx cp.
You can change to another project where you wanted to work by running the command . It brings up 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".