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Installation Guide

Contents

We currently support installation on Linux (tested on Ubuntu and CentOS) and Mac OSX. We do not currently support Windows.

There are three possible ways to install UMI-tools: conda, pip or from source, in decending order of ease.

Note

As of version 1.0.0 UMI-tools requires python 3.5 or better. If you are still using python 2.7, we recommend you switch to python 3. If you use conda it is possible to have both python 2 and python 3 environments. If you can't do this and really need 2.7, we recommend you use UMI-tools 0.5.5, but note that this will not be updated.

Quick Start

Try one of the following:

$ conda install -c bioconda -c conda-forge umi_tools

or:

$ pip install umi_tools

or grab a zip of the latest release from github and unpack (replace 0.5.5 with version number; replace wget with curl -O for OS X):

$ unzip 1.0.0.zip
$ cd UMI-tools-1.0.0
$ python setup.py install --user

If these options don't work, see below.

Conda package manager

This is the easiest way to install UMI-tools if you are already using either anaconda python or miniconda: all depedencies, whether they be python libraries or system libraries are automatically installed. You can also do all your installations in seperate isolated "environments" where installing new software will not affect packages in other environments. The downside of conda installation is that if you do not already use anaconda or miniconda, you will be building a completely new python environment, would have to reinstall all of your libraries etc. You can read more about conda here.

  1. Install miniconda (if not already installed), see conda installation instructions here.

  2. Type:

    $ conda install -c bioconda -c conda-forge umi_tools

That's it, simple as that.

Installation from PyPI using the pip package manager

The pip python pacakge manager is the standard package manager. The advantage over conda is that it is probably already installed on your system, will use your existing python environments, and plays nicely with the virtualenv system. On the downside, the installation of dependencies is not handled as cleanly as in conda. You will need

  • python version greater than 3.5
  • gcc or compatible c compiler
  • zlib with development headers
  • the pip python package manager version at least 1.4

Linux

Most systems will already have gcc, pip and zlib installed, so its worth just trying:

$ pip install umi_tools

If you also have python 2 on your system, you may need to use pip3 rather than pip. If you get a permissions error try adding --user to the pip command. Note that umi_tools will now only be installed for the current user.

If that doesn't work, then you need to find what is missing. You can check for gcc and pip by typing gcc or pip at a terminal prompt. Installing GCC and zlib is much easier if you have root access on your machine. In the unlikely event that you don't have these installed AND you don't have root access, please speak to someone who does have root access. Python and pip can be installed without root.

  1. Install gcc: the easiest way is using your package manager. In ubuntu or debian:

    $ sudo apt-get install gcc

    or in CentOS/Redhat/Fedora:

    $ sudo yum install gcc

  2. Install zlib: again, use the package manager. Ubuntu:

    $ sudo apt-get zlib1g-dev

    or in CentOS/Redhat/Fedora:

    $ sudo yum install zlib-devel

  3. Install pip: pip is also probably available from your package manager. In ubuntu, Centos, RHEL and fedora the package is called python-pip. In CentOS/RHEL the package is located in the EPEL repository which needs to be installed first. You could also install pip from the web:

    $ wget https://bootstrap.pypa.io/get-pip.py
$ python get-pip.py --user

    but in this case you'll need to make sure that the python-dev (Ubuntu) or python-devel (CentOS/RHEL/fedora) packages are installed.

The pip command at the top should now work.

Apple OS X

The good news is that zlib is installed by default of OS X. The bad news is that gcc and pip are generally not included (although many users may have installed them already). Furthermore, it's generally not advisable to use the default python since installation of third party python libraries leads to difficulties with permissions, especially since the introduction of System Integrity Protection (SIP) from OS X El Capitan onwards. For this reason, we recommend using a non-default python.

If you only have the default python (e.g /usr/local/bin/python) there are a number of ways to install another instance of python. Many OS X users recommend using the homebrew package manager to manage command line packages on OS X. You can find instructions here for installation python via homebrew. This will also install setuptools and pip. You can install gcc via homebrew by following these instructions:

$ brew install gcc48

You may also need to install freetype:

$ brew install freetype

Install UMI-tools: You should now have everything you need to install UMI-tools:

$ pip install umi_tools

We have had reports that the current version of one of the UMI-tools dependencies, pysam, is causing problems on the latest versions of OS X. If your installation is failing on the installation of pysam, try forcing an older version with:

$ pip install pysam==0.8.4

before installing umi_tools.

If you don't want to do use homebrew, here are non-homebrew instructions for installing gcc and pip as needed:

  1. Install gcc: Apples XCode suite includes gcc. Installation depends on which version of OS X you are using

    • Mac OS X 10.9 or higher: Open a terminal and run:

      $ xcode-select --install

    • Mac OS X 10.8 or lower: go to Apple's developer download page and download Command Line Tools for XCode. You'll need a developer account.

  2. Install pip: In a terminal type:

    $ curl -O https://bootstrap.pypa.io/get-pip.py
$ python get-pip.py

Installing from source

There are several reaons you might want to install from source. If for example you need to install the most up-to-date version, or if you can't or don't want to use one of the package managers above. There are two levels of installing from source. The first is to install the dependencies using one of the pacakge managers above, and then just install umi_tools from source. The second is to install everything from source without the help of pip or conda.

Depedencies from conda/PyPI manager

  1. Download the UMI-tools code, either the latest release or the master branch (which should contain the lastest development version) and unpack the zip or tar and enter the directory:

    $ unzip 1.0.0.zip
$ cd UMI-tools-1.0.0

    or clone the repository:

    $ git clone https://github.com/CGATOxford/UMI-tools.git

  1. Use your python package manager to install the dependencies. e.g. for pip

    $ pip install -r requirements.txt

    or with conda:

    $ conda install setuptools
$ conda install pandas
$ conda install future
$ conda install scipy
$ conda install matplotlib
$ conda config --add channels bioconda
$ conda install regex
$ conda install pysam

  2. Install UMI-tools using the setup.py script:

    $ python setup.py install --user

Completely from source

Warning

This section is deprecated and no longer updateed. Once upon a time it was possible for us to provide complete instructions for installing completely from source without a package manager. Unfortunately, our dependencies have multiplied and the dependencies of our dependencies have also multiplied. You can try the below and it may work as the system libraries required are not particularly rare, especially if you are already doing bioinformatics. However, if one of the dependencies fails to install, I'm afraid you are on your own.

This method will allow you to install without installing pip or conda. It is in theory possible to install completely without root by installing gcc, zlib and python-dev in your home directory, but that is beyond the scope of this document. You are also going to need a g++ compatiable compiler. On OS X XCode has one of these by default. On Linux install the build-essential or g++ packages.

  1. Download and install Cython. For OS X replace wget with curl -O:

    $  wget https://pypi.python.org/packages/c6/fe/97319581905de40f1be7015a0ea1bd336a756f6249914b148a17eefa75dc/Cython-0.24.1.tar.gz
 $ tar -xzf Cython-0.24.1.tar.gz
 $ cd Cython-0.24.1.tar.gz
 $ python setup.py install --user

  2. Download and install UMI-tools:

    $ wget https://github.com/CGATOxford/UMI-tools/archive/master.zip
$ unzip master.zip
$ cd UMI-tools-master
$ python setup.py install --user

    running this is probably going to take quite a long time. You will probably see quite a lot of warning messages that look like errors.

    The most likely fail point is installing pysam. Due to a bug in pysam, when it is installed from source, the recorded install version is wrong. Thus, if you get the error:

    $ pysam 0.2.3 is installed by 0.8.4 is required by umi_tools

    try just running setup again.

    In addition, as we pointed out above, we have had reports that installation of the lastest pysam fails on the latest OS X. If this is the case, try installing an older version of pysam:

    $ curl -O https://pypi.python.org/packages/27/89/bf8c44d0bfe9d0cadab062893806994c168c9f490f67370fc56d6e8ba224/pysam-0.8.4.tar.gz
$ tar -xzf pysam-0.8.4.tar.gz
$ cd pysam-0.8.4
$ python setup.py install --user

Running tests

After installing from source you can run the test suite to make sure everything is working. To do this you'll need to install nose and pyyaml using your favourite package manager and then run:

$ nosetests tests/test_umi_tools.py

Getting further help

If you are still having trouble with installation, contact us by by creating an issue on our github issues page.