Installation

illumiprocessor requires the installation of JAVA, trimmomatic, and illumiprocessor. The instructions below assume you are either:

  1. running osx
  2. running linux (x86_64 or osx)

We do not support any other platforms, although you should be able to install and run illumiprocessor and its dependencies on various flavors of windows.

JAVA

Illumiprocessor uses trimmomatic, which is a JAVA program. As a result, you need to install JAVA for your platform. Getting JAVA installed is tricky across various platforms and largely beyond the scope of this document, but here are some very general directions for installing JAVA 1.7, which is best suited for illumiprocessor, along several other codebases that we use (e.g. current GATK).

Apple OS X

To install JAVA 1.7, download and install the package from Oracle here: http://www.java.com/en/download/manual.jsp

CentOS linux

You can install the JRE with the following yum command:

su -c "yum install java-1.7.0-openjdk"

Ubuntu linux

You can install the JRE with the following apt-get command:

sudo apt-get install openjdk-7-jre

trimmomatic & illumiprocessor

You can install the remaining dependencies in one of two ways: (1) using conda and (2) manually. We strongly suggest that you use conda, which is part of the anaconda python distribution. There are several reasons for this, one being that we can manage lots of types of packages with conda. Another is that conda manages dependencies of packages very, very well.

The use of anaconda in our lab is the default.

Installation using conda

If you are using anaconda and/or the conda package manager, you can automatically install everything you need by editing ~/.condarc to add the faircloth-lab binstar repository, so that the file looks like:

# channel locations. These override conda defaults, i.e., conda will
# search *only* the channels listed here, in the order given. Use "default"
# to automatically include all default channels.

channels:
  - defaults
  - http://conda.binstar.org/faircloth-lab

Then run:

conda install illumiprocessor

This will install trimmomatic and illumiprocessor in standardized locations that will work in a number of situations. It will also test the installations to ensure they were installed corrected.

The trimmomatic jar file is installed into your $ANACONDA_HOME/jar.

“Manual” installation

Of course, you can install illumiprocessor in the standard (manual) way. As above you need to ensure that you have:

  1. installed JAVA
  2. installed trimmomatic

Once those are completed, you can download the illumiprocessor, then run:

python setup.py install

The illumiprocessor binary will be where your python distribution stores binaries, and the libraries will be in the site-packages directory for your $PYTHONPATH.

Caution

You will need to manually specify the path to trimmomatic when you run illumiprocessor