smithy

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

1. Install Python 3.11: https://www.python.org/downloads/
2. Install BLAST 2.16: 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/
   • Download the win64 version: ncbi-blast-2.16.0+-win64.exe
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 (should be set automatically)
   • e.g. C:\Program Files\NCBI\blast-2.16.0+\bin
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. Add the following folders to smithy-app\smithy:
   • media
   • media\images
   • media\csv
8. In command prompt, navigate to smithy-app/smithy
9. Run the app-setup powershell script, or alternatively run steps 10-11.
10. Run the django database migrations:
    • python manage.py makemigrations
    • python manage.py migrate
    • python manage.py makemigrations assembly
    • python manage.py migrate
11. Prepare static files:
    • python manage.py collectstatic
12. Run the app:
    • python manage.py runserver