How to install BioMAJ?


  • git: installation here.
  • virtualenv

Then, create your BioMAJ directory:

mkdir biomaj310
cd biomaj310

Clone all git repositories of the BioMAJ project:

git clone
git clone
git clone
git clone
git clone
git clone
git clone 
git clone
git clone
git clone
git clone

Create a Python virtual environment to install BioMAJ and every associated package:

virtualenv envtest310

Every time you will want to use BioMAJ you have to activate the Python virtual environment:

source envtest310/bin/activate

Getting out of the virtual environment :



Installation of each BioMAJ modules:

for repertoire in $(ls |grep "biomaj"); 
    do echo $repertoire; 
    cd $repertoire; git pull; 
    python install; 
    cd .. ; 

Package installation:

pip install requests
pip install redis
pip install influxdb
pip install pyyaml
cd biomaj
pip install -r requirements.txt
cd ..

Creation of a directory necessary for the proper functioning of BioMAJ:

mkdir tmp/
mkdir tmp/mongo
mkdir tmp/biomaj
mkdir tmp/biomaj/conf # configuration file
mkdir tmp/biomaj/db # data storage
mkdir tmp/biomaj/log # log files
mkdir tmp/biomaj/lock # bank lock files 
mkdir tmp/biomaj/process
mkdir tmp/biomaj/cache

Mongodb installation for ubuntu, short version(more information):

tar xvzf mongodb-linux-x86_64-3.4.0.tgz
<home>/mongodb-linux-x86_64-3.4.0/bin/mongod --dbpath <home>/tmp/biomaj/db/ &


You are ready to start, go to Tutorial.