How to install BioMAJ?

Requirements:

  • git: installation here.
  • virtualenv

Then, create your BioMAJ directory:

mkdir biomaj310
cd biomaj310

Clone all git repositories of the BioMAJ project:

git clone https://github.com/genouest/biomaj-zipkin.git
git clone https://github.com/genouest/biomaj-user.git
git clone https://github.com/genouest/biomaj-cli.git
git clone https://github.com/genouest/biomaj-process.git
git clone https://github.com/genouest/biomaj-download.git
git clone  https://github.com/genouest/biomaj.git
git clone https://github.com/genouest/biomaj-daemon.git 
git clone https://github.com/genouest/biomaj-watcher.git
git clone https://github.com/genouest/biomaj-ftp.git
git clone https://github.com/genouest/biomaj-release.git
git clone https://github.com/genouest/biomaj-core.git

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 :

deactivate

 

Installation of each BioMAJ modules:

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

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 bank.properties
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):

wget https://fastdl.mongodb.org/linux/mongodb-linux-x86_64-3.4.0.tgz
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.