#!/bin/bash
# BASH shell script to run viga in a docker container. 
# Saved as /usr/local/bin/run-viga
# 
# Notes:
#
# 1. Input files are assumed to be present in the directory where
#    this command is run.
# 2. Other viga options can be specified and are sent as is
# 3. User must have either 
#    a. sudo access to run this script (script should be run as sudo run-viga) or 
#    b. user must be part of the docker group
# 4. Default user is viga

echo "Running command: python /program/VIGA.py $*"

# Get current user
CURRENT_USER=$(logname)

# Get current user id
CURRENT_UID=$(id -u ${CURRENT_USER})

# Run container
docker run --rm \
       -e LOGNAME=${CURRENT_USER} \
       -e USER=${CURRENT_USER} \
       -u ${CURRENT_UID}:${CURRENT_UID} \
       -v /data/databases:/data/databases:ro \
       -v $(pwd):/wdir \
       -w /wdir \
       vimalkvn/viga python /program/VIGA.py $*