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10x Genomics
Chromium Genome & Exome

Long Ranger Installation

Long Ranger 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 GRCh37 and GRCh38 reference packages required for Long Ranger are provided as separate downloads.

Download and Install

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

$ cd /opt
[ download file from downloads page ]
$ tar -xzvf longranger-2.2.2.tar.gz

This unpacks Long Ranger, its dependencies, and an environment setup script into a new directory called longranger-2.2.2.

Step 2 – Download and unpack the reference data file in a convenient location:

[ download file from downloads page ]
$ tar -xzvf refdata-hg19-2.1.0.tar.gz

This creates a new directory called refdata-hg19-2.1.0 that contains the hg19 reference and a set of pre-generated indices and other data required by Long Ranger.

Step 3 – Prepend the Long Ranger directory to your $PATH. This will allow you to invoke the longranger commands.

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

$ export PATH=/opt/longranger-2.2.2:$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 Long Ranger will run smoothly once you have generated your own Chromium data. Assuming you have installed and entered the 10x environment as described above, please run the following commands:

$ longranger sitecheck > sitecheck.txt
$ longranger upload your@email.edu sitecheck.txt

If you plan to run Long 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 support@10xgenomics.com.

Verify Installation

To ensure that the longranger pipeline is installed correctly, use longranger testrun. This test can take up to 60 minutes on a sixteen-core workstation. Assuming you have installed Long Ranger into /opt, the command to run the test would look like:

$ export PATH=/opt/longranger-2.2.2:$PATH
$ longranger testrun --id=tiny
 
longranger testrun 2.2.2
Copyright (c) 2016 10x Genomics, Inc.  All rights reserved.
-----------------------------------------------------------------------------
Martian Runtime - 2.3.2
 
Running preflight checks (please wait)...
2016-05-01 12:00:00 [runtime] (ready)           ID.tiny.VCALLER_CS.VCALLER.CANONICALIZE_GROUND_TRUTH
2016-05-01 12:00:00 [runtime] (run:local)       ID.tiny.VCALLER_CS.VCALLER.CANONICALIZE_GROUND_TRUTH.fork0.split
...
2016-05-01 12:39:09 [runtime] (chunks_complete) ID.tiny.VCALLER_CS.VCALLER.SUMMARIZE_REPORTS
2016-05-01 12:39:09 [runtime] (join_complete)   ID.tiny.VCALLER_CS.VCALLER.SUMMARIZE_REPORTS
 
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:

$ longranger upload your@email.edu tiny/tiny.mri.tgz

If your system does not have direct Internet connectivity, you can also send the file as an attachment to support@10xgenomics.com.