smithy

Follow these steps to set up the application on your machine.

1. Install Python 3.8: https://www.python.org/downloads/
2. Install BLAST 2.11 (newer versions may work): https://blast.ncbi.nlm.nih.gov/Blast.cgi
   • Install and user manual here: https://www.ncbi.nlm.nih.gov/books/NBK569861/
   • Windows install and configuration instructions here: https://www.ncbi.nlm.nih.gov/books/NBK52637/
3. Configure BLAST user environment variables to their defaults
   • BLASTDB = "C:\your\db\path"
   • BLASTDB_LMDB_MAP_SIZE = 1000000
   • Add the BLAST+ bin path to the user's Path environment variable
4. Copy the provided BLAST (addgene, dnasu, igem) sequence db files into database folder (same as the BLASTDB environment variable)
   • Example db path: "C:\NCBI\db"
5. Add the project path to a PYTHONPATH user environment variable
   • Example: PYTHONPATH = "C:\your\path\smithy-app"
6. Run a pip install of requirements.txt:
   • pip install -r requirements.txt
7. In command prompt, navigate to smithy-app/smithy
8. Run the django database migrations:
   • python manage.py makemigrations
   • python manage.py migrate
   • python manage.py makemigrations assembly
   • python manage.py migrate
9. Run the app:
   • python manage.py runserver