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README.md

README

USER INFO

Instigator

name: Jean-Michel Garant

email: jean-michel.garant@usherbrooke.ca

gitlab username: J-Michel

REPO INFO

gitlab url: gitlabscottgroup.med.usherbrooke.ca/J-Michel/g4rna_screener

Version: G4RNA screener 0.3

Please consider cloning/downloading a stable branch

DEPENDENCIES

Here are listed dependencies in format:

library_name (recommended version)
From environment
python2.7 (2.7.15rc1)
From Python

Available from pip

biopython (1.68)
numpy (1.11.0)
pandas (0.18.1)
PyBrain (0.3)
regex (2016.9.22)
scipy (0.18.1)

mysql-connector-python (2.1.4) is also highly recommended for automated retrieval of information on UCSC and Ensembl databases using -c, --columns arguments. It is not available through pip but here are the steps to follow to install it:

sudo -i
cd PATH/TO/PYTHON/dist-packages/    or    cd PATH/TO/PYTHON/site-packages/
wget https://dev.mysql.com/get/Downloads/Connector-Python/mysql-connector-python-2.1.4.tar.gz --no-check-certificate
tar -xzf mysql-connector-python-2.1.4.tar.gz
cd mysql-connector-python-2.1.4
python setup.py install

Consider adding G4RNA screener to your environment path

Example for a bash terminal

cd PATH/TO/g4rna_screener
echo "" >> ~/.bashrc
echo "# add G4RNA screener to PATH" >> ~/.bashrc
echo "export PATH=\"\$PATH:$(pwd)\"" >> ~/.bashrc
source ~/.bashrc

GLOSSARY