# 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`, `dx cd`, `dx mv`, and `dx cp`, which let you list objects, change folders, move data objects, and 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`](/user/helpstrings-of-sdk-command-line-utilities.md#ls). ```shell $ 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`. ```shell $ 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. ```shell $ 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. ```shell $ 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. ```shell $ 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](/user/objects/searching-data-objects.md#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`](/user/helpstrings-of-sdk-command-line-utilities.md#cd). ```shell $ 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`](/user/helpstrings-of-sdk-command-line-utilities.md#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`. ```shell $ 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`). ```shell $ 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. ```shell $ 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.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](/developer/api/regions.md) through `dx cp`. ## Changing Your Current Project ### Changing 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`](/user/helpstrings-of-sdk-command-line-utilities.md#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". ```shell $ 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`: ```shell $ 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. ```shell $ 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]`: ```shell $ dx select project-9zVfbG2y8x65kxKY7x20005G Selected project project-9zVfbG2y8x65kxKY7x20005G $ dx ls -l Project: Mouse (project-9zVfbG2y8x65kxKY7x20005G) Folder : / ``` --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://documentation.dnanexus.com/user/projects/project-navigation.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.