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10x Genomics
Chromium Single Cell CNV

Cell Ranger DNA Installation

Cell Ranger DNA is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its own required software dependencies, which are pre-compiled to run on a wide range of Linux distributions.

For convenience, the reference data package required for Cell Ranger DNA is provided as a separate download.

Download and Install

Step 1 – Download and unpack the Cell Ranger DNA file in any location. In this example we use /opt.

$ cd /opt
[ download file from downloads page ]
$ tar -xzvf cellranger-dna-1.1.0.tar.gz

This unpacks Cell Ranger DNA, its dependencies, and the cellranger-dna script into a new directory called cellranger-dna-1.1.0.

Step 2 – Download and unpack any of the reference data files in a convenient location:

[ download file from downloads page ]
$ tar -xzvf refdata-GRCh38-1.0.0.tar.gz

This creates a new directory called refdata-GRCh38-1.0.0 that contains a single reference (in this case, GRCh38/Ensembl). Each reference contains a set of pre-generated indices and other data required by Cell Ranger DNA.

Step 3 – Prepend the Cell Ranger DNA directory to your $PATH. This will allow you to invoke the cellranger-dna command.

If you unpacked both Cell Ranger DNA and the reference data into /opt, then you would run the following command:

$ export PATH=/opt/cellranger-dna-1.1.0:$PATH

You may wish to add this command to your .bashrc for convenience.

Site Check Script

Next, please run the bundled site check script and send the output to 10x. We will review the information to ensure that Cell Ranger DNA will run smoothly once you have generated your own Chromium data. Assuming you have installed Cell Ranger DNA as described above, please run the following commands:

$ cellranger-dna sitecheck > sitecheck.txt
$ cellranger-dna upload [email protected] sitecheck.txt

If you plan to run Cell Ranger DNA on a cluster, please run and send us the output twice, once on a submit host and once on a cluster node.

If your system does not have direct Internet connectivity, please send the output files as attachments to [email protected].

Verify Installation

To ensure that the cellranger-dna pipeline is installed correctly, use cellranger-dna testrun. This test requires approximately 512 MB of free memory and can take up to 10 minutes running on a single core. Assuming you have installed Cell Ranger DNA into /opt, the command to run the test would look like:

$ export PATH=/opt/cellranger-dna-1.1.0:$PATH
$ cellranger-dna testrun --id=tiny
cellranger-dna testrun 1.1.0
Copyright (c) 2016 10x Genomics, Inc.  All rights reserved.
Martian Runtime - 3.2.1
Running preflight checks (please wait)...
2018-04-26 14:12:20 [runtime] (ready)           ID.tiny.CNV_CALLER_SINGLECELL_CS.CNV_CALLER_SINGLECELL._ALIGNER.SETUP_CHUNKS
2018-04-26 14:12:20 [runtime] (run:local)       ID.tiny.CNV_CALLER_SINGLECELL_CS.CNV_CALLER_SINGLECELL._ALIGNER.SETUP_CHUNKS.fork0.chnk0.main
Pipestance completed successfully!

Whether the test pipestance succeeds or fails, you will then see:

Saving diagnostics to tiny/tiny.mri.tgz

This tiny.mri.tgz file contains diagnostic information 10x can use to help resolve any problems. It is generated whether the pipeline succeeds or fails. If the pipeline fails and you need troubleshooting assistance, you can send this file directly to us from the command line:

$ cellranger-dna upload [email protected] tiny/tiny.mri.tgz

If your system does not have direct Internet connectivity, you can also send the file as an attachment to [email protected].