Installation

System requirements

  • Any Java-enabled platform (Windows, Linux, Mac OS X)
  • Java version 7 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

  • Check that you have Java 1.7+ installed on your system by typing java -version. Here is the example output of this command:

    > java -version
java version "1.7.0_65"
Java(TM) SE Runtime Environment (build 1.7.0_65-b17)
Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)

  • unzip the archive with MiXCR

  • 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 1.7+ installed on your system by typing java -version

  • unzip the archive with MiXCR

  • 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.