10XGenomics/cellranger: 10x Genomics Single Cell 3′ Gene Expression and VDJ Assembly

Build dependencies

  • Python 2.7.13
  • rust 1.28.0
  • clang 6.0
  • go 1.11
  • node v8.11.4

Example setup of build dependencies on Ubuntu 16.04.3

sudo apt-get install make clang-6.0 golang-1.11-go libz-dev libbz2-dev liblzma-dev # Add golang to path export PATH=/usr/lib/go-1.11/bin:$PATH # Install rustup from https://www.rustup.rs/ . Then: rustup install 1.28.0 rustup default 1.28.0

Build command


Runtime dependencies

Setting up the environment

# Setup Martian and binary dependencies source /path/to/ranger/sourceme.bash # Setup Cell Ranger source /path/to/cellranger/sourceme.bash

Note about Loupe

The binaries required to generate Loupe Cell Browser (.cloupe) and Loupe V(D)J Browser files (.vloupe) are not included in this repository or in the binary dependencies package Ranger. The necessary binaries can be obtained from an existing binary version of Cell Ranger by running: cp /path/to/cellranger-3.0.2/cellranger-cs/*/lib/bin/ /path/to/open-source-cellranger/lib/bin/

We do not provide support for building and running this code.

The officially supported release binaries are available at: (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest)


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