Installation

System requirements

  • Any Java-enabled platform (Windows, Linux, Mac OS X)
  • Java version 8 or higher (download from Oracle web site)
  • 1–16 Gb RAM (depending on number of clones in the sample)

Installation on Mac OS X / Linux using Homebrew

Homebrew is a simple package manager developed for Mac OS X and also ported to Linux. To install MiXCR using Homebrew just type the following commands:

brew tap milaboratory/all
brew install mixcr

Installation on Mac OS X / Linux / FreeBSD from zip distribution

  • Check that you have Java 1.8+ installed on your system by typing java -version. Here is the example output of this command:

    > java -version
java version "1.8.0_66"
Java(TM) SE Runtime Environment (build 1.8.0_66-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)

  • download latest binary distributaion of MiXCR from the release page on GitHub

  • unzip the archive

  • add extracted folder of MiXCR distribution to your PATH variable or add symbolic link for mixcr script to your bin/ folder (e.g. ~/bin/ in Ubuntu and many other popular linux distributions)

Installation on Windows

Currently there is no execution script or installer for Windows. Still MiXCR can easily be used by direct execution from the jar file.

  • check that you have Java 1.8+ installed on your system by typing java -version

  • download latest binary distributaion of MiXCR from the release page on GitHub

  • unzip the archive

  • use mixcr.jar from the archive in the following way:

    > java -Xmx4g -Xms3g -jar path_to_mixcr\jar\mixcr.jar ...

For example:

> java -Xmx4g -Xms3g -jar C:\path_to_mixcr\jar\mixcr.jar align input.fastq.gz output.vdjca

To use mixcr from jar file one need to substitute mixcr command with java -Xmx4g -Xms3g -jar path_to_mixcr\jar\mixcr.jar in all examples from this manual.