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Release Notes

v1.1.0 - First PIP release, updated readme docs v1.0.0 - Initial release of open source code base

Instructions for developers

Testing

Several unit tests were written for py.test. From your virtual environment, run the following command from the repository root folder.

python -m pytest

Tests are automatically run via CircleCI. Results are located at https://circleci.com/gh/synthego-open/ice.

Building the docker image locally

Requirements:

From a command line

git clone git@github.com/synthego-open/ice.git ice # clone the repo
cd ice
docker build . -t ice # build the image from the Dockerfile

Running the examples

Running a single ICE analysis:

docker run -it -v ${PWD}:/data -w /ice -i ice:latest \
	python ice_analysis_single.py\
	--control /data/ice/tests/test_data/good_example_control.ab1 \
	--edited /data/ice/tests/test_data/good_example_edited.ab1 \
	--target AACCAGTTGCAGGCGCCCCA \
	--out /data/results/testing \
	--verbose

Running a batch analysis:

docker run -it -v ${PWD}:/data -w /ice -i ice:latest \
	python ice_analysis_batch.py\
	--in /data/ice/tests/test_data/batch_example.xlsx \
	--data /data/ice/tests/test_data/ \
	--out /data/results/ \
	--verbose

Installing locally from repository

Requirements:

  • Python 3.X (last tested on 3.6, via anaconda)

Installation

Install your favorite python3 virtual environment (virtualenv, conda). We'll use conda for this example.

conda create --name ice_env python=3 # create a python3 virtual environment
source activate ice_env

git clone git@github.com/synthego-open/ice.git ice # clone the repo
cd ice

pip install -r requirements.txt # install the python dependencies

Running the examples

Running a single ICE analysis:

./ice_analysis_single.py \
	--control ./ice/tests/test_data/good_example_control.ab1  \
	--edited ./ice/tests/test_data/good_example_edited.ab1 \
	--target AACCAGTTGCAGGCGCCCCA \
	--out results/testing \
	--verbose

Running a batch analysis:

./ice_analysis_batch.py \
	--in ./ice/tests/test_data/batch_example.xlsx \
	--out ./results/ \
	--data ./ice/tests/test_data/
	--verbose