- Python 2.7
- Virtualenv (recommended)
# CLONE THE REPOSITORY FROM GITHUB
git clone https://github.com/zxqwerxz/epi_pyscripts.git
# CREATE A VIRTUALENV TO INSTALL REQUIRED PYTHON DEPENDENCIES
cd epi_pyscripts
virtualenv env
. env/bin/activate
pip install -r requirements.txt
# EVERY TIME YOU WANT TO RUN SOMETHING FROM THE PACKAGE, RUN:
. env/bin/activate
# EVERY TIME YOU ARE FINISHED WITH THE PACKAGE, RUN:
deactivate
I recommend making symlinks so you do not need to copy the python scripts everywhere. Here is an example:
# LET'S ASSUME YOU HAVE YOUR DATA HERE
cd /home/jyzhou/data/project1
# CREATE A SYMLINK
ln -s /path/to/epipyscripts src
# NOW YOU CAN RUN THE SCRIPTS LIKE THIS:
python src/fetch_seq.py infile.csv human > outfile.fastq