cloud-init-bioconductor-image.sh

#!/bin/bash

set -x

# Cloud init used during VM initialize on image created previously using Packer
PATH=$PATH;PATH+=":/bin" ;PATH+=":/usr/bin";PATH+=":/usr/sbin";PATH+=":/usr/local/bin"; 
dirname=$(dirname $0)
cd "$dirname"
dirname=$(dirname pwd)
PATH+=":$dirname"
export PATH

CONF_DIR="$dirname"/../conf
LIB_DIR="$dirname"/../lib

# Set owner as root for debian ssh key to avoid login. Einfra account from metadata should be used to mount NFS storage.
# Uncomment here when finished development
chown root: /home/debian/.ssh/authorized_keys

# True to use deploy key or any other to download public repo
PRIVATE_REPO=""

echo "------------------------"
echo "Checking Debian OS version versus github bio-class repository version"
tmp_req_ver=9
tmp_req_repo="bio-class"
tmp_ver=$(cat /etc/debian_version | cut -f 1 -d '.')
echo "DEBIAN VERSION $tmp_ver"
echo "BIO-CLASS VERSION $tmp_req_ver"

# Set SSH Warning Message to Users
tmp_issuenet=$(sudo cat /etc/issue.net)
if [[ $tmp_ver -ne $tmp_req_ver ]];then
echo -e "####################################################################
#                                                                  #
# ERROR - DEBIAN IS VERSION $tmp_ver BUT FOR SELECTED BIOCONDUCTOR IS REQUIRED VERSION $tmp_req_ver #
#                                                                  #
#                                                                  #
# UNABLE TO CONTINUE, EXITING CUSTOM CLOUD INIT SCRIPT FOR $tmp_req_repo #
#                                                                  #
####################################################################" > /etc/issue.net
  echo "------------------------"
  echo "ERROR - DEBIAN IS VERSION $tmp_ver" BUT FOR SELECTED BIOCONDUCTOR IS REQUIRED VERSION $tmp_req_ver
  echo "UNABLE TO CONTINUE, EXITING CUSTOM CLOUD INIT SCRIPT FOR $tmp_req_repo"
  echo "------------------------"
else
echo -e "####################################################################
#                                                                  #
# Instance is during process of software instalation, please wait! #
#                                                                  #
# Login will be enabled after finished configuration.              #
#                                                                  #
####################################################################" > /etc/issue.net
fi

sed -i 's/#Banner none$/Banner \/etc\/issue.net/g' /etc/ssh/sshd_config
systemctl restart sshd

if [[ $tmp_ver -ne $tmp_req_ver ]];then
  echo "Exiting from CUSTOM CLOUD INIT SCRIPT FOR BIOCONDUCTOR"
  exit 1
fi

# Backup repo
if [[ -d /home/debian/bio-class ]];then
  mv /home/debian/bio-class /home/debian/bio-class-backup
fi

cd /home/debian/;

if [[ "$PRIVATE_REPO" == "true" ]];then

  set +x

  # Using deploy key to access Github private repository
  # Private key for deploy key, NOT your personal private key!
  # This part is not necessary if repository public
  echo -e "-----BEGIN RSA PRIVATE KEY-----
...INSERT PRIVATE KEY AS DEPLOY KEY HERE...
-----END RSA PRIVATE KEY-----" > /root/.ssh/id_rsa

  # Public key for deploy keys
  # This part is not necessary if repository public
  echo -e "...INSERT PUBLIC KEY FOR DEPLOY KEY HERE..." > /root/.ssh/id_rsa.pub

  echo -e "# GitLab.com server
Host gitlab.com
RSAAuthentication yes
IdentityFile /root/.ssh/id_rsa
StrictHostKeyChecking no
UserKnownHostsFile=/dev/null" > ~/.ssh/config

  set -x

  cd /root/
  chmod 700 .ssh/
  chmod 644 .ssh/authorized_keys
  chmod 644 .ssh/known_hosts
  chmod 644 .ssh/id_rsa.pub
  chmod 600 .ssh/id_rsa

  # Start SSH agent
  eval $(ssh-agent -s)
  ssh-add /root/.ssh/id_rsa
  # SSH Host Key Checking
  ssh-keyscan -H github.com >> /root/.ssh/known_hosts

  #test connection
  ssh -T git@github.com
  # test deploy key Fingerprint
  ssh-add -l -E md5

  # Clone repository
  cd /home/debian/;
  git clone git@github.com:bio-platform/bio-class.git 2>&1 > /home/debian/gitclone.txt

  # Delete deploy key
  rm -rf /root/.ssh/id_rsa*

  # Deletes all identities from the agent
  ssh-add -D

else
  # Clone public repo
  git clone https://github.com/bio-platform/bio-class.git 2>&1 > /home/debian/gitclone.txt

fi


# Cloned repository
cd /home/debian/;
if [[ ! -d /home/debian/bio-class ]];then
  if [[ -d /home/debian/bio-class-backup ]];then
    echo "ERROR to clone repository, using repository from image"
    mv /home/debian/bio-class-backup /home/debian/bio-class
  fi
else
  if [[ -d /home/debian/bio-class-backup ]];then
    rm -rf /home/debian/bio-class-backup
  fi
fi

# List if cloned successfully
ls -la /home/debian/bio-class

# Change to repository
cd /home/debian/bio-class/install;

# Install software
chmod +x ./install_software.sh
./install_software.sh -m pre 2>&1 | tee /home/debian/install_software_pre.txt
./install_software.sh -m post 2>&1 | tee /home/debian/install_software_post.txt

# Install patch if difference between image/upstream repository versions
if [[ -f ./install_software_patch.sh ]];then
  chmod +x ./install_software_patch.sh
  ./install_software_patch.sh 2>&1 | tee /home/debian/install_software_patch.txt
fi

echo "# Remove SSH Warning Message to Users after finished Software instalation"
sudo sh -c "echo ${tmp_issuenet} > /etc/issue.net"
sudo sed -i 's/Banner.*/#Banner none/g' /etc/ssh/sshd_config
sudo systemctl restart sshd

exit 0