- The latest releases can be obtained from our GitHub:
- The latest development pre-builds can be downloaded from:
Linux / MacOS
Download and extract
Create a folder where you want to install MiXCR and navigate to that folder. Bellow is the command that creates
mixcrfolder in your home directory.
> mkdir ~/mixcr > cd ~/mixcr
Go to MiXCR GitHub page and copy the link for latest build. The command bellow downloads MiXCR v4.3.2. For other builds replace the link with the one you obtained from GitHub.
Unpack the zip archive using the
unzipcommandThe output looks similar to this:
> unzip mixcr-4.3.2.zip
Archive: mixcr-4.3.2.zip inflating: mixcr inflating: LICENSE inflating: mixcr.jar
mixcrworks with the following command
> ~/mixcr/mixcr -v
The output should look similar to:
MiXCR v4.3.2 (built Tue Apr 11 20:35:07 CEST 2023; rev=123d699964; branch=no_branch; host=fv-az364-276) RepSeq.IO v1.8.0-21-master (rev=5521c5842b) MiLib v2.4.0-7-master (rev=acea8397fe) Built-in V/D/J/C library: repseqio.v2.2 Library search path: - built-in libraries - /Users/imyarek/mixcr-4.3.2/.
Add MiXCR to your
MiXCR is now installed. To run it requires entering the path to the executable command on the command line. We want to be able to run MiXCR by simply entering the word
mixcron the command line. To accomplish this, we add it to your $PATH variable. Go into the directory where you unpacked
pwd.The output will be the full path to MiXCR directory
> cd ~/mixcr/ > pwd
Then use the export command to add it into the $PATH variable.
Add export to bash.rc file
It is better to add that command to your
.bashrcfile, so you won't have to repeat it every time you start a new session.
echo "export PATH=/home/user/mixcr:$PATH" >> ~/.bashrc
MiXCR has Anaconda repository to simplify installation of MiXCR using
conda package manager. To install the latest stable MiXCR build with conda run:
> conda install -c milaboratories mixcr
to install a specific version run:
> conda install -c milaboratories mixcr=3.0.12
mixcr package specifies
openjdk as a dependency, if you already have Java installed on your system, it might be a good idea to prevent conda from installing another copy of JDK, to do that use
> conda install -c milaboratories mixcr --no-deps
MiXCR has a Homerew formula to simplify installation of MiXCR using
brew package manager.To install the latest stable MiXCR build with brew run:
> brew tap milaboratory/all
> brew install mixcr
Go to MiXCR GitHub page and download the latest build.
Unpack the zip archive in the folder where you want MiXCR to be installed. You will see several file:
For demonstration purposes lets use
mixcr LICENSE mixcr.jar
Open terminal and execute the following command
shell java -jar C:\mixcr\mixcr.jar -v
If everything is fine you will see an output similar to:MiLib v2.0.0-11-master (rev=ca59a3ad71) Built-in V/D/J/C library: repseqio.v2.0 ```
MiXCR v4.3.0 (built Fri Mar 17 17:26:47 CET 2023; rev=96be4ef48c; branch=no_branch; host=fv-az262-972) RepSeq.IO v1.8.0 (rev=ce36405897) MiLib v2.4.0 (rev=95ac7c4c41) Built-in V/D/J/C library: repseqio.v2.2