- 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)
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
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 formixcr
script to yourbin/
folder (e.g.~/bin/
in Ubuntu and many other popular linux distributions)
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
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.