ViewBovine Server - oxfordfun/ViewBovine GitHub Wiki

Access to server

1. use SSH:

   ssh [email protected]

2. Attach to tmux session:

   tmux a

Observe tmux windows:

0 - openvpn
1 - ViewBovine web server
2 - tree api
3 - map api

Update Cattle DB

Create a new window: C-b n

1. Update sample name - guid map table

   curl http://localhost:5008/sync_sample_lookup_table

2. Clean map data with clean.py

   cd ~/apha/getree/clean/ python3 clean.py Cattle_db_20190311_113500.tsv > Cattle_db_20190311_113500-CLEAN.tsv

3. Generate distance matrix

   cd ~/apha/getree/ python3 mk_outcsv.py Cattle_db_20190311_113500-CLEAN.tsv > ~/map-api/meta/out_20190311_113500.tsv

4. Restart map-api with new data files

   python3 main.py --map_file 'meta/Cattle_db_20190311_113500-CLEAN.tsv' --movement_file 'meta/Cattle_movement_20190311_113900.tsv' --distance_file 'meta/out_20190311_apha.tsv'

5. Submit new trees to be generated:

   cd ~/apha/getree/ python3 mktrees.py --out_csv_file meta/out_20190311_apha.tsv --map_file meta/Cattle_db_20190311_113500-CLEAN.tsv --regen_best_guids

6. Restart getree cd ~/apha/getree/ python3 main.py