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10x Genomics Single Cell 3' Gene Expression and VDJ Assembly
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README.md

Building Cell Ranger 3.0.2

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

make

Running Cell Ranger

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/{crconverter,vlconverter} /path/to/open-source-cellranger/lib/bin/

Support

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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