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If your question is not answered here, please email us at:  ${email.software} # 10x GenomicsChromium Single Cell Gene Expression # Cell Ranger Installation Cell Ranger is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its 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 is provided as a separate download. ## Download and Install Step 1 – Download and unpack the Cell Ranger file in any location. In this example we use /opt. $ cd /opt
$tar -xzvf cellranger-3.0.2.tar.gz  This unpacks Cell Ranger, its dependencies, and the cellranger script into a new directory called cellranger-3.0.2. Step 2 – Download and unpack any of the reference data files in a convenient location: [ download file from downloads page ]$ tar -xzvf refdata-cellranger-GRCh38-3.0.0.tar.gz


This creates a new directory called refdata-cellranger-GRCh38-3.0.0 that contains a single reference (in this case, GRCh38). Each reference contains a set of pre-generated indices and other data required by Cell Ranger.

$cellranger upload [email protected] sitecheck.txt  If you plan to run Cell Ranger 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 pipeline is installed correctly, use cellranger testrun. This test can take up to 60 minutes on a sixteen-core workstation. Assuming you have installed Cell Ranger into /opt, the command to run the test would look like: $ export PATH=/opt/cellranger-3.0.2:$PATH$ cellranger testrun --id=tiny

cellranger testrun 3.0.2
-----------------------------------------------------------------------------
Martian Runtime - v3.2.0

2016-11-14 09:57:54 [runtime] (split_complete)  ID.tiny.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SETUP_CHUNKS
...

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 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].