SNDG web to show argentinian COVID19 isolates
* Python 3.7 + Pip , VirtualEnv recommended
* Docker
* Environment variables
* export DJANGO_READ_DOT_ENV_FILE=True
* $DB_PASS
* .env
git clone https://github.com/sndg-arg/covid19-web.git
cd covid19-web
virtualenv -p python3.7 env
source env/bin/activate
pip install -r requirements/local.txt # or production#https://jbrowse.org/docs/embedding.html
wget "https://github.com/GMOD/jbrowse/releases/download/1.16.6-release/JBrowse-1.16.6.zip"
unzip JBrowse-1.16.6.zip
rm JBrowse-1.16.6.zip
mv JBrowse-1.16.6/ data/jbrowse
sed -i 's|c.src=function(t){return i.p+""+|c.src=function(t){return "/static/jbrowse/"+i.p+""+|' data/jbrowse/dist/browser.bundle.js
mkdir data/jbrowse/data# Install Javascript dependencies
mkdir data/tmp/
chmod -R 777 data/tmp/
docker run -u $(id -u):$(id -g) -v ${PWD}/data/tmp/.npm:/.npm --rm -v $PWD:/out -w /out node:lts npm install
# Fix old libraries
sed -i 's|require("bootstrap/js/tooltip.js")|require("bootstrap/js/dist/tooltip.js")|' ./node_modules/feature-viewer/lib/index.js
sed -i 's|require("bootstrap/js/popover.js")|require("bootstrap/js/dist/popover.js")|' ./node_modules/feature-viewer/lib/index.js
# Build javascript dependency
docker run -u $(id -u):$(id -g) --rm -v $PWD:/out -w /out node:lts npm run-script build- DB
- Postgres Engine
docker run -v $PWD/data/sndgr:/var/lib/postgresql/data --name sndgr \
-e POSTGRES_PASSWORD=$DB_PASS -e POSTGRES_DB=sndgr -p 5432:5432 -d \
--shm-size 512m postgres:11* Base data
./manage.py migrate
mkdir data/tmp
./manage.py init_db
./manage.py import_genome -i data/curated/covid19.gb -a "COVID19" -n "COVID19" -t 2697049
./manage.py update_covid_data
# check
docker exec -u postgres -it sndgr psql
> \l
> \c sndgr
> \dt
* Annotation
mkdir data/pdb
./manage.py pdbfiles2pdbdb # change PDBfiles path with "pdbs_dir" parameters
./manage.py fpocket2pdbdb* Load genome in JBrowse
* ./manage.py db2jbrowse --dbname COVID19
* Create admin user
* ./manage.py createsuperuser
- Load variants data
./manage.py process_covid_msa -i data/curated/test.fasta --override-
Cross variants with PDB residues and remove obsolete** ./manage.py update_covid_pdb
-
Start server ./manage.py runserver
-
Development
- ./manage.py makemessages -l es -l en -i -v 3 "env/*" # env in case you have an virtualenv there
- ./manage.py shell_plus --ipython --print-sql # interactive ipython shell
-
Production
- export DJANGO_SETTINGS_MODULE=config.settings.production
- mkdir data/static
- ./manage.py collectstatic
- docker exec sndgr pg_dump -U postgres sndgr | gzip > ./2020_06_02_covid.sql.gz
- zcat ./2020_06_02_covid.sql.gz | docker exec -i sndgr psql -U postgres -d covid -
- scp -r ./sndg_covid19/static/auto/posfigs server:deploy/covid19-web/data/static/auto/posfigs