cdot.cc install log

Install REST server

sudo bash
apt-get update
apt-get upgrade -y

apt-get install -y git-core python3-venv redis nginx

# Users and source code

SYSTEM_CDOT_USER=cdot
CDOT_REST_INSTALL_DIR=/opt/cdot_rest

id -u ${SYSTEM_CDOT_USER} &>/dev/null || useradd ${SYSTEM_CDOT_USER} --create-home --shell "/bin/bash"
mkdir -p ${CDOT_REST_INSTALL_DIR}
chown ${SYSTEM_CDOT_USER} ${CDOT_REST_INSTALL_DIR}
chgrp ${SYSTEM_CDOT_USER} ${CDOT_REST_INSTALL_DIR}

su ${SYSTEM_CDOT_USER}
CDOT_REST_INSTALL_DIR=/opt/cdot_rest  # Again for user
cd ${CDOT_REST_INSTALL_DIR}
if [ ! -e ${CDOT_REST_INSTALL_DIR}/.git ]; then
    git clone https://github.com/sacgf/cdot_rest.git .
fi

# Install Python libraries
mkdir venv
python3 -m venv venv/cdot
source /opt/cdot_rest/venv/cdot/bin/activate
python3 -m pip install --upgrade pip
python3 -m pip install gunicorn # Install into venv so it gets libraries
python3 -m pip install -r requirements.txt

Services

# As root
mkdir /var/log/cdot_rest
chown cdot /var/log/cdot_rest
mkdir /run/gunicorn
chown cdot /run/gunicorn/

cp config/gunicorn.service /lib/systemd/system
systemctl enable gunicorn

Inserting data

Either download the data, or see cdot instructions on how to create data from scratch

# Virtual environment
sudo su cdot
cd /opt/cdot_rest
source venv/cdot/bin/activate

Insert data

python3 manage.py import_transcript_json cdot-0.2.8.refseq.grch37_grch38.json.gz --annotation-consortium=RefSeq
python3 manage.py import_transcript_json cdot-0.2.8.ensembl.grch37_grch38.json.gz --annotation-consortium=Ensembl