How to install biomaj?

Create your BioMAJ directories:

mkdir data/
mkdir data/conf
mkdir data/lock
mkdir data/db
mkdir data/process
mkdir data/cache
mkdir data/log

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

virtualenv envtest310

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

source envtest310/bin/activate

Getting out of the virtual environment :

deactivate

Pip and requests installation:

pip install --upgrade pip
easy_install pip
pip uninstall requests
easy_install requests

Installation of all required packages for BioMAJ (specifications for Ubuntu, it may require adpatations for another OS):

apt-get install libssl-dev libcurl4-openssl-dev python-dev
cd biomaj
pip install -r requirements.txt
cd ..

Creation of the configuration file and addition of an example to test the BioMAJ installation:

cd biomaj
cp global.properties.example global.properties
#Copy the example of the bank alu:
cp biomaj/tests/alu.properties <your path>/tmp/biomaj/conf 
#Modify root.dir in the global.properties file to match the path of all your data (<your path>/tmp/biomaj): 
vim global.properties
cd ..

Specific indications for pycurl (for CentOS):

git clone https://github.com/genouest/biomaj.git
cd biomaj
pip install -r requirements.txt
cp global.properties.example global.properties
#Copy the example of the bank alu:
cp biomaj/tests/alu.properties <your path>/data/conf 
#Modify root.dir in the global.properties file to match the path of all your data (<your path>/data): 
vim global.properties
#For Ubuntu
apt-get install libssl-dev libcurl4-openssl-dev python-dev
cd ..

Specific indications for pycurl (for CentOS):

pip install pycurl==7.43.0.1 --global-option="--with-nss"

Or for Ubuntu:

easy_install pycurl

If you want more information or if you have ssl issues : http://pycurl.io/docs/latest/install.html#ssl

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

sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 0C49F3730359A14518585931BC711F9BA15703C6
echo "deb [ arch=amd64,arm64 ] http://repo.mongodb.org/apt/ubuntu xenial/mongodb-org/3.4 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-3.4.list
sudo apt-get update
sudo apt-get install -y mongodb-org
sudo service mongod start

An other example for mongodb installation for CentOS (Thanks to the Plateforme Auvergne Bioinformatique):


vi mongodb.repo
yum repolist
yum install mongodb-org.x86_64
systemctl status mongod
systemctl start mongod
mongo

Installation of the BioMAJ packages:

pip install biomaj-cli
pip install biomaj-daemon
pip install biomaj-user
pip install biomaj-download
pip install biomaj-process
pip install biomaj-cron
pip install biomaj-ftp

For biomaj-watcher :

git clone https://github.com/genouest/biomaj-watcher
cd biomaj-watcher
python setup.py develop

You can quickly test your installation with these commands:

# from the biomaj directory or by specifying the location of the global.properties file (--config option):
cd biomaj
biomaj-cli.py --help
biomaj-cly.py --bank alu --update

You are ready to start, go to Tutorial.