Project and Data Object 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 (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.

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 on 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.

Note that we enclosed our path with quotes (" "), so dx interprets the spaces as part of 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 which match a pattern

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 asterix and the spaces in the path.

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

Switching Contexts

Changing folders

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 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, 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.

$ 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 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.

$ 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. 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.

$ dx select project-BQpp3Y804Y0xbyG4GJPQ01xv Selected project project-BQpp3Y804Y0xbyG4GJPQ01x $ 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.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 will automatically be copied recursively.

Note ! that 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 cloud regions through dx cp.

Changing Your Current Project

Change to another project with a project prompt list

You can change to another project where you wanted to work by running the command dx select. 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".

$ 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 : /

Change to a public project

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

$ dx select --public Available public projects: 0) dxvg-integration (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

Change to a project with VIEW permission

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.

$ 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

Change 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 : /

Last edited by Steve Osazuwa, 2017-06-27 18:49:38