Installing the software required for the OneCellPipe system

Here are more detailed instruction for installing and running the OneCellPipe software and its requirements. These instructions are for a Linux Ubuntu system where you have sudo rights, please adjust accordingly if you are using a different flavor of a Unix-based operating system! This is a sub-page of the multi-page documentation for the OneCellPipe pipeline of OneCellBio.

Installation

1. If necessary, update your system and install Python 2 and build packages – or ask your system administrator for it if you are not allowed to run sudo commands.
   python –version should show something like:
   Python 2.7.12

   sudo apt update
   sudo apt install -y python build-essential

2. If necessary, update / install Java 8 or ask your system administrator for it.

   sudo apt install -y default-jre --fix-missing

3. Install NextFlow

   wget -qO- get.nextflow.io | bash
   

   You can of course use curl if wget is not available. In order to run the software from anywhere in the file system move it to a directory specified in your path settings:
   

   sudo mv nextflow /usr/local/bin/

   or add the current location to your path if you do not have sudo permissions. For the bash shell this could be:
   

   echo export PATH=$PATH:$PWD >> ~/.bashrc; source ~/.bashrc

   You can print out your current path settings with: echo $PATH

4. Install Singularity
   We are using the version 2.5.1 at this time (check other versions here, but there might occur format incompatibilities). The installation of Singularity requires sudo rights to work properly.

   VERSION=2.5.1
   wget https://github.com/singularityware/singularity/releases/download/$VERSION/singularity-$VERSION.tar.gz
   tar xvf singularity-$VERSION.tar.gz
   cd singularity-$VERSION
   ./configure --prefix=/usr/local
   make
   sudo make install
   cd ..
   rm singularity-$VERSION.tar.gz

   In case there is an error like “configure: error: Unable to find the libarchive headers”, please also install:
   

   sudo apt install -y libarchive-dev

5. Install the OneCellBio pipeline
   We are using the current version 1.21, adjust if necessary.

   VERSION=1.21
   wget https://s3.amazonaws.com/gt-datastorage/onecellpipe/onecellpipe.$VERSION.tgz
   tar xzf onecellpipe.$VERSION.tgz
   rm onecellpipe.$VERSION.tgz

Run the test pipeline

Use the sample data provided to test that everything is working:

cd ~/onecellpipe
nextflow onecellpipe.nf --dir sampledata

This will start the process producing out like the following:

N E X T F L O W  ~  version 0.27.0
Launching `onecellpipe.nf` [lonely_ekeblad] - revision: 4daa120f75

======================================
O N E C E L L B I O    P I P E L I N E
======================================
Pipeline  version : 1.21
Pipeline directory: /home/ubuntu/onecellpipe

Project directory : sampledata
Log file path     : /home/ubuntu/onecellpipe/sampledata/indrop_log.txt
Timestamp         : Mon Jan 15 12:29:08 UTC 2018

[warm up] executor > local
[18/fe30f8] Submitted process > setup (Setup procedure)

This will run in about 5-20 minutes, depending on your number of CPUs/core. An example timeline for a machine with 8 cores can bee seen here.
You can interrupt and end the pipeline by hitting <Ctrl>C.
You can try to resume the pipeline by adding -resume to your command.