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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 dx ls.$ dx ls
Developer Quickstart/
Developer Tutorials/
Quickstart/
RNA-seq Workflow Example/
SRR100022/
_README.1st.txt
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
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.$ 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
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.$ dx ls "project-BQpp3Y804Y0xbyG4GJPQ01xv:/C. Elegans - Ce10/*.fasta*"
ce10.fasta.fai
ce10.fasta.gz
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
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
...
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.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 will automatically be copied recursively.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 cloud regions throughdx cp.
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 : /
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) 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
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
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 modified 2mo ago