Building Cell Ranger 3.0.2.9001

This version of cellranger has minor changes for compatibility with current software releases. It builds cellranger 3.0.2 with minor modifications to run without errors. This is not an officially supported release but aims to give the same results as cellranger 3.0.2 for testing pipelines which require cellranger to be installed.

A docker image is available:

https://github.com/TomKellyGenetics/cellranger_clean

https://hub.docker.com/r/tomkellygenetics/cellranger_clean

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 18.04.4 LTS (Bionic Beaver)

sudo apt-get install make clang-6.0 libz-dev libbz2-dev liblzma-dev

# install go-1.11 from source as not available for Ubuntu 18.04
wget https://dl.google.com/go/go1.11.linux-amd64.tar.gz
tar -xvf go1.11.linux-amd64.tar.gz \
sudo mv go /usr/local
export GOROOT=/usr/local/go
export GOPATH=$HOME/go
export PATH=$GOPATH/bin:$GOROOT/bin:$PATH
sudo ln -s /usr/lib/go-1.11/bin/go /usr/bin/go

# Add golang to path
export PATH=/usr/lib/go-1.11/bin:$PATH

# Install rustup from https://www.rustup.rs/ and configure Rust
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh  -s -- -y
sudo apt-get install -y libstd-rust-1.40 cargo
ENV PATH /root/.cargo/bin/:$PATH
ENV PATH  $HOME/.cargo/bin:$PATH
RUN bash $HOME/.cargo/env

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh  -s -- -y

#RUN apt-get install -y libstd-rust-1.40 cargo
export PATH=/root/.cargo/bin/:$PATH
export PATH=$HOME/.cargo/bin:$PATH
bash $HOME/.cargo/env
rustup install 1.40.0
rustup default 1.40.0

Build command

git clone https://github.com/TomKellyGenetics/cellranger.git cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001  \
 && cd cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001 \
 && make && make louvain-clean &&  make louvain \
 && cd -

Set up directory structure to match 10x tar release

ln -s cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/bin/cellranger cellranger-3.0.2.9001/cellranger \

Set up paths to cellranger. This is most of what sourceme.bash would do.

export PATH=$PWD/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/bin/:$PWD/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/bin:$PWD/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/tenkit/bin/:$PWD/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/tenkit/lib/bin:/martian/bin/:$PATH
export PYTHONPATH=$PWD/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/lib/python:$PWD/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/tenkit/lib/python:$PWD/martian/adapters/python:$PYTHONPATH
export MROPATH=$PWD/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/mro/:$PWD/cellranger-3.0.2.9001/cellranger-cs/3.0.2.9001/tenkit/mro/
export _TENX_LD_LIBRARY_PATH=whatever

Running Cell Ranger

Runtime dependencies

• Binary dependencies can be found in the Ranger 3.0.2 package (https://support.10xgenomics.com/developers/software/downloads/latest)
  • The Ranger package includes a build of the Martian platform (v3.2.0), which is open source. For more information, go to http://martian-lang.org/ .

The dependences can be installed from source:

# Install node.js
curl -sL https://deb.nodesource.com/setup_13.x | bash - \
 && apt-get install -y nodejs

# Install Martian. Note that we're just building the executables, not the web stuff
RUN git clone --recursive https://github.com/martian-lang/martian.git \
 && cd martian \
 && make mrc mrf mrg mrp mrs mrstat mrjob
 
# Install bcl2fastq. mkfastq requires it.
RUN apt-get update \
 && apt-get install -y alien unzip wget \
 && wget https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2-19-1-linux.zip \
 && unzip bcl2fastq2*.zip \
 && alien bcl2fastq2*.rpm \
 && dpkg -i bcl2fastq2*.deb \
 && rm bcl2fastq2*.deb bcl2fastq2*.rpm bcl2fastq2*.zip

# Install STAR aligner
RUN wget https://github.com/alexdobin/STAR/archive/2.5.1b.tar.gz \
 && tar xf 2.5.1b.tar.gz \
 && rm 2.5.1b.tar.gz \
 && cd STAR-2.5.1b \
 && make \
 && mv bin/Linux_x86_64_static/STAR* /usr/bin \
 && cd .. \
 && rm -rf STAR-2.5.1b

# Install tsne python package. pip installing it doesn't work
RUN git clone https://github.com/mckinsel/tsne.git \
 && cd tsne \
 && make install \
 && cd .. \
 && rm -rf tsne

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)