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10x Genomics
Chromium De Novo Assembly

Installation

Supernova 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 range of Linux distributions.

Download and Install

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

$ cd /opt
[ download file from downloads page ]
$ tar -xzvf supernova-2.1.1.tar.gz

This unpacks Supernova, its dependencies, and the supernova script into a new directory called supernova-2.1.1.

Step 2 – Prepend the Supernova directory to your $PATH. This will allow you to invoke the supernova command.

$ export PATH=/opt/supernova-2.1.1:$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 Supernova will run smoothly once you have generated your own Chromium data. Assuming you have installed Supernova as described above, please run the following commands:

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

If your system does not have direct Internet connectivity, please send the output files as attachments to support@10xgenomics.com.

Verify Installation

To ensure the Supernova pipeline is installed correctly, use supernova testrun. This test can take up to 20 minutes on a sixteen-core workstation. Assuming you installed Supernova into /opt, the necessary commands would look like:

$ export PATH=/opt/supernova-2.1.1:$PATH
$ supernova testrun --id=tiny
 
supernova testrun 2.1.1
Copyright (c) 2016 10x Genomics, Inc.  All rights reserved.
-----------------------------------------------------------------------------
Running Supernova in test mode.
Martian Runtime - v2.3.3
 
Running preflight checks (please wait)...
2016-05-03 11:17:00 [runtime] (ready)           ID.tiny.ASSEMBLER_CS._ASSEMBLER._ASSEMBLER_PREP.SETUP_CHUNKS
2016-05-03 11:17:03 [runtime] (split_complete)  ID.tiny.ASSEMBLER_CS._ASSEMBLER._ASSEMBLER_PREP.SETUP_CHUNKS
2016-05-03 11:17:03 [runtime] (run:local)       ID.tiny.ASSEMBLER_CS._ASSEMBLER._ASSEMBLER_PREP.SETUP_CHUNKS.fork0.chnk0.main
...
2016-05-03 11:20:36 [runtime] (run:local)       ID.tiny.ASSEMBLER_CS._ASSEMBLER.ASSEMBLER_CP.fork0.join
2016-05-03 11:20:39 [runtime] (join_complete)   ID.tiny.ASSEMBLER_CS._ASSEMBLER.ASSEMBLER_CP
 
Outputs:
- Run summary:        /home/jdoe/runs/sample345/outs/summary.csv
- Run report:         /home/jdoe/runs/sample345/outs/report.txt
- Raw assembly files: /home/jdoe/runs/sample345/outs/assembly
 
Pipestance completed successfully!

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

Saving pipestance info 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:

$ supernova 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.