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‎.gitignore

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.env
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build
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dist
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dnada.egg-info

‎backend/app/LICENSE

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Apache License
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‎backend/app/MANIFEST.in

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include README.md LICENSE

‎backend/app/README.md

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# DNAda
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DNAda is a web application that integrates the [j5](https://j5.jbei.org)
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DNA assembly software with robotic liquid handlers.
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## Background
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J5 is a powerful DNA assembly software that can be used to design
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and optimize DNA assembly protocols. However, it is not directly compatible with
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robotic liquid handlers. DNAda is a web/command-line application
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that integrates j5 with robotic liquid handlers by converting a
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j5 assembly design into a series of liquid handler compatible instructions.
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This enables a user without progamming experience to design DNA assembly
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protocols on a user-friendly
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canvas, [DeviceEditor](https://j5.jbei.org/DeviceEditor_manual/index.html),
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and then convert the design using J5 and subsequently DNAda into a series
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of instructions that can be executed on a liquid handler.
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## CLI Installation
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Note, it is highly recommended to use a virtual environment to install the dependencies.
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For example,
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```bash
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wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
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bash Mambaforge-$(uname)-$(uname -m).sh
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source ~/mambaforge/bin/activate
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mamba create -y -n dnada
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conda activate dnada
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mamba install -y python==3.11
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```
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```bash
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pip install dnada
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```
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Alternatively, setup from the source code by running
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```bash
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git clone https://github.com/JBEI/dnada.git
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cd dnada/backend/app
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python setup.py install
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```
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Note, there is [currently a bug](https://github.com/autoprotocol/autoprotocol-python/pull/396)
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in autoprotocol-python. To temporarily resolve this bug until it gets patched, identify the
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location of the autoprotocol library identified in your virtual environment and apply the
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fix-oligosynthesizeolig-serialization.patch file. For example,
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```bash
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cd ~/mambaforge/envs/dnada/lib/python3.11/site-packages/
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patch -p1 < ~/dnada/backend/app/fix-oligosynthesizeoligo-serialization.patch
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```
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## Quick Start
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There is a sample J5 design file available in the `examples/` directory in the github repo.
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After installing the DNAda CLI through pip or github, to run DNAda on that design file,
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execute:
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```bash
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cd dnada/examples
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dnada_cli example_j5_output.zip
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```
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After a few seconds you should see a new `.zip` archive generated with the
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name `automation_instructions.zip`.

‎setup.py ‎backend/app/setup.py

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from setuptools import setup, find_packages
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import os
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import io
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DESCRIPTION = (
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"An application for creating customized "
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"synthetic biology automation instructions"
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)
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here = os.path.abspath(os.path.dirname(__file__))
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try:
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with io.open(os.path.join(here, "README.md"), encoding="utf-8") as f:
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long_description = "\n" + f.read()
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except FileNotFoundError:
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long_description = DESCRIPTION
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setup(
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name="dnada",
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version="0.1",
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version="0.1.2",
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maintainer="Alberto Nava",
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maintainer_email="[email protected]",
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description=(
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"An application for creating customized "
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"synthetic biology automation instructions"
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),
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description=DESCRIPTION,
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long_description=long_description,
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long_description_content_type="text/markdown",
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url="https://github.com/JBEI/dnada",
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packages=find_packages(where=os.path.join("backend", "app", "app")),
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package_dir={"": os.path.join("backend", "app", "app")},
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packages=find_packages(),
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classifiers=[
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"Programming Language :: Python :: 3",
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"License :: OSI Approved :: Apache Software License",

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