Installation

The latest releases can be obtained from our GitHub:: https://github.com/milaboratory/mixcr/releases/
The latest development pre-builds can be downloaded from:: https://link.milaboratory.com/software/mixcr/mixcr-develop.zip

Linux / MacOS

Manual installation

Download and extract mixcr:

Create a folder where you want to install MiXCR and navigate to that folder. Bellow is the command that creates mixcr folder 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 v4.1.2. For other builds replace the link with the one you obtained from GitHub.
```
wget https://github.com/milaboratory/mixcr/releases/download/v4.2.0/mixcr-4.2.0.zip
```

Unpack the zip archive using the unzip command

> unzip mixcr-4.2.0.zip

The output looks similar to this:

Archive:  mixcr-4.2.0.zip
  inflating: mixcr
  inflating: LICENSE
  inflating: mixcr.jar

Check that mixcr works with the following command

> ~/mixcr/mixcr -v

The output should look similar to:

MiXCR v4.2.0 (built Thu Jan 26 20:40:26 CET 2023; rev=b0f194e0c6; branch=no_branch; host=fv-az477-60)
RepSeq.IO v1.7.0 (rev=36f4e4453f)
MiLib v2.3.0 (rev=0226f1da59)
Built-in V/D/J/C library: repseqio.v2.1

Library search path:
- built-in libraries
- /Users/user/dir/.

Add MiXCR to your $PATH:

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 mixcr on the command line. To accomplish this, we add it to your $PATH variable. Go into the directory where you unpacked mixcr and enter pwd.
```
> cd ~/mixcr/
> pwd
```
The output will be the full path to MiXCR directory
```
/home/user/mixcr
```
Then use the export command to add it into the $PATH variable.
```
export PATH=/home/user/mixcr:$PATH
```
Add export to bash.rc file

It is better to add that command to your .bashrc file, so you won't have to repeat it every time you start a new session.
```
echo "export PATH=/home/user/mixcr:$PATH" >>  ~/.bashrc 
```

Anaconda package

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 --no-deps flag:

> conda install -c milaboratories mixcr --no-deps

Homebrew formula

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

Windows

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 C:\mixcr\ folder.
```
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:

MiXCR v (built Fri Jul 15 01:51:38 CEST 2022; rev=aa769be87b; branch=tag-rework-2; host=Dmitrys-MacBook-Pro-2.local)
RepSeq.IO v1.4.1-1-master (rev=474ebe0f6e)
MiLib v2.0.0-11-master (rev=ca59a3ad71)
Built-in V/D/J/C library: repseqio.v2.0