#!/bin/bash
# setupuser
if [ "$#" -ne 2 ]; then
  echo "Usage: $0 USERNAME QMASTERHOST" >> /tmp/azuredeploy.log.$$
  exit 1
fi
DOCKERUSER=$1
QMASTERHOST=$2
# Pull Docker image
docker pull myoshimura080822/galaxy_in_docker_bitwf:160607
# Galaxy Singleuser
mkdir -p /home/${DOCKERUSER]/work/github/
cd /home/${DOCKERUSER]/work/github/
git clone https://github.com/manabuishii/docker-galaxy-singleuser.git
cd docker-galaxy-singleuser
curl -s -o ./job_conf.xml.sge.docker https://raw.githubusercontent.com/manabuishii/azure-files/master/scripts_for_setup/galaxy_SGE/job_conf.sge.docker
# data directory
#
# mkdir -p data/transcriptome_ref_fasta
# mkdir -p data/adapter_primer
# mkdir -p data/Homo_sapiens_genome
# mkdir -p data/Mus_musculus_genome
mkdir data
cd data
curl -s -o ./dl.sh https://raw.githubusercontent.com/manabuishii/azure-files/master/scripts_for_setup/galaxy_SGE/dl.sh
chmod 755 dl.sh
./dl.sh
cd ..
# export directory
mkdir -p export/postgresql/
chmod 777 -R export


Add master setup script for using SGE and Docker
Add master setup script for using SGE and Docker
