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Manual install

Helixer

Predmoter works hand in hand with Helixer. There are two scripts from Helixer that are necessary for Predmoter to work: fasta2h5.py, used to create the h5 files from fasta files, and add_ngs_coverage.py, can be found in helixer/evaluation and is used to add NGS data (bam files) to an existing h5 file created with fasta2h5.py for training and/or testing. The built-in functions to convert fasta to h5 files are also used by Predmoter to predict on fasta files without the user having to convert them manually.

Get the code

Predmoter

# clone via HTTPS
git clone https://github.com/weberlab-hhu/Predmoter.git

# allows access via SSH
git clone [email protected]:weberlab-hhu/Predmoter.git

Helixer

# clone via HTTPS
git clone https://github.com/weberlab-hhu/Helixer.git

# allows access via SSH
git clone [email protected]:weberlab-hhu/Helixer.git

Virtual environment (optional)

The installation of all the python packages in a virtual environment is recommended: https://docs.python-guide.org/dev/virtualenvs/, https://docs.python.org/3/library/venv.html.

For example, create and activate an environment called "env":

python3 -m venv env
source env/bin/activate
# install everything

# deactivation
deactivate

Installation

# Helixer
cd Helixer
pip install -r requirements.txt
cd ..

# Predmoter
cd Predmoter
pip install -r requirements.txt
pip install .  # or 'pip install -e .', if you will be changing the code

# Helixer 
# force Helixer installation to be the manual one
cd ../Helixer
pip install .  # or 'pip install -e .', if you will be changing the code