Usage

1. Clone this repository (with git clone)

2. Put data in input_data/. There are 3 type of files:

   • input_data/gene/result_gene_<phecode>.txt.gz
     • format: tab-delimited, including a header row
       • columns: GeneName, Start_Pos, End_Pos, NumofRareVariants, MAC_Case, MAC_Control, Case, Control, p.value
       • eg, A3GALT2 1:33306784:I:6 1:33312867:C:T 44 11 732.000087726994 114 11286 0.365819488062416
   • input_data/variant/result_singlevariant_<phecode>.txt.gz
     • format: tab-delimited, including a header row
       • columns: GeneName, SNP, MAF, MAC_Case, MAC_Control, p.value
       • eg, A3GALT2 1:33306784:I:6 1.1e-04 0 5 8.3e-01
   • input_data/phenotype-info.csv (already included in repo)

3. Run python3 -m pip install -r requirements.txt (or, if running for only your own user, python3 -m pip --user install -r requirements.txt)

4. Run python3 make_sqlite3_db.py (inside the genes-site subdirectory) to produce assoc.db

5. Run python3 make_tables.py to produce static/phenotypes.json and static/genes.json

6. Run python3 make_variant_sqlite3_db.py to produce variant.db

7. Run the server using one of these:

   • python3 serve.py (insecure and slow, for development/debugging)
   • gunicorn serve:app -k gevent -w4 --bind 0.0.0.0:5000 (fast, for production)

   Then open http://localhost:5000 in your web browser to access the site. If you are running the site on a remote computer, first start an ssh tunnel (like ssh -L 5000:localhost:5000 <user>@<server>) if on Mac/Linux or follow directions if on Windows.

8. To deploy your changes to the server:

   • If you changed the data in input_data, copy them to the server's directory /home/pjvandehaar/genes-site/input_data.
   • If you changed the files assoc.db, static/phenotypes.json, static/genes.json, or variant.db, copy them to /home/pjvandehaar/genes-site/genes-site on the server (and replace the files currently there), or just run the commands to re-generate them on the server.
   • Run git push to push your code to GitHub, and then on the server run cd /home/pjvandehaar/genes-site && sudo git pull && sudo systemctl restart gunicorn-genes-site.