Setup and Install Cellranger
Download and Install
Step 1 – Download and unpack the Cell Ranger file in any directory. In this an example, we use $HOME/opt.
mkdir -p $HOME/opt
cd $HOME/opt
# Download from 10xgenomics
tar -xzvf cellranger-3.1.0.tar.gz
Step 2 – Download and unpack any of the reference data files in any convenient directory:
mkdir -p $HOME/opt/refdata
cd $HOME/opt/refdata
curl -O http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-mm10-3.0.0.tar.gz
tar zxvf refdata-cellranger-mm10-3.0.0.tar.gz
Step 3 – Prepend the Cell Ranger directory to your $PATH. This will allow you to invoke the cellranger command.
If you unpacked both Cell Ranger and the reference data into $HOME/opt, then you would run the following command:
export PATH=$HOME/opt/cellranger-3.1.0:$PATH
You may wish to add this command to your $HOME/.bashrc for convenience.
Verify the 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 $HOME/opt, the command to run the test would look like the following:
export PATH=$HOME/opt/cellranger-3.1.0:$PATH
cellranger testrun --id=tiny
cellranger testrun 3.1.0
Copyright (c) 2016 10x Genomics, Inc. All rights reserved.
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Martian Runtime – v3.2.3
Running preflight checks (please wait)…
2016-11-14 09:57:51 [runtime] (ready) ID.tiny.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SETUP_CHUNKS
2016-11-14 09:57:54 [runtime] (split_complete) ID.tiny.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SETUP_CHUNKS
…
Pipestance completed successfully!