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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