This version of GDM was created on a Ubuntu system and should be able to be deployable to most Virtualbox and Vagrant versions for your systems. If there are deployment issues please reach out to Roy Petrie [ rlp243@cornell.edu ]
Software Requirements
Virtualbox [ Download ]
This is the virtual software used to host the virtual machine.
Vagrant [ Download ]
This software uses an image repository for the automated Virtual Machine creation.
Git [ Windows Download ]
This is the software used to clone the repository.
Please verify you have completed the above requirements fully before attempting to deploy scGDM on your local machine.
Steps to Deploy scGDM
Please note: These steps have been created using a Linux Ubuntu system and are planned to be expanded for Mac & Windows Users.
1.) Create a workspace that can be used to host the repository. In this the location ~/workspace directory will be used. This location can exist anywhere but please make sure to notate its location.
cd ~/ && mkdir workspace && cd ~/workspace
2.) Clone the git repo
git clone https://bitbucket.org/gobiiproject/gobii.deploy.vagrant.git
3.) Change directories into gobii.deploy.vagrant/
4.) Within this location there are 2 files you should see:
Vagrantfile
provision/setup.sh
5.) Run the following command within the gobii.deploy.vagrant directory:
At this point vagrant will start a download of the image within the vagrant cloud repo.
The output for this command should show the following:
Output Text
rpetrie @ bytz [~/workspace/gobii.deploy.vagrant] (develop) $ time vagrant up
Bringing machine 'default' up with 'virtualbox' provider...
==> default: Importing base box 'gadm/scGDM'...
==> default: Matching MAC address for NAT networking...
==> default: Checking if box 'gadm/scGDM' is up to date...
==> default: Setting the name of the VM: scgdm-server
==> default: Clearing any previously set network interfaces...
==> default: Preparing network interfaces based on configuration...
default: Adapter 1: nat
default: Adapter 2: bridged
==> default: Forwarding ports...
default: 22 (guest) => 2222 (host) (adapter 1)
==> default: Running 'pre-boot' VM customizations...
==> default: Booting VM...
==> default: Waiting for machine to boot. This may take a few minutes... default: SSH address: 127.0.0.1:2222
default: SSH username: vagrant default: SSH auth method: private key
default:
default: Vagrant insecure key detected. Vagrant will automatically replace
default: this with a newly generated keypair for better security.
default:
default: Inserting generated public key within guest...
default: Removing insecure key from the guest if it's present...
default: Key inserted! Disconnecting and reconnecting using new SSH key...
==> default: Machine booted and ready!
==> default: Checking for guest additions in VM...
==> default: Setting hostname...
==> default: Configuring and enabling network interfaces...
==> default: Mounting shared folders...
default: /vagrant => /mnt/28ada824-b37f-4d2b-9a6e-5a7bbd45b656/Cloud_Storage/google_drive/works
pace/gobii.deploy.vagrant
==> default: Running provisioner: shell...
default: Running: /tmp/vagrant-shell20200602-15241-aqqjrn.sh
default: + sudo apt update
default:
default: WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
default: Hit:1 http://us.archive.ubuntu.com/ubuntu bionic InRelease
default: Get:2 http://us.archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB]
default: Get:3 https://download.docker.com/linux/ubuntu bionic InRelease [64.4 kB]
default: Get:4 http://us.archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]
default: Get:5 http://us.archive.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB]
default: Get:6 http://us.archive.ubuntu.com/ubuntu bionic-updates/main amd64 Packages [951 kB]
default: Get:7 https://download.docker.com/linux/ubuntu bionic/stable amd64 Packages [12.1 kB]
default: Get:8 http://us.archive.ubuntu.com/ubuntu bionic-updates/main Translation-en [324 kB]
default: Get:9 http://us.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 Packages [1,07
7 kB]
default: Get:10 http://us.archive.ubuntu.com/ubuntu bionic-updates/universe Translation-en [335
kB]
default: Get:11 http://us.archive.ubuntu.com/ubuntu bionic-security/main amd64 Packages [727 kB
]
default: Get:12 http://us.archive.ubuntu.com/ubuntu bionic-security/main Translation-en [230 kB
]
default: Get:13 http://us.archive.ubuntu.com/ubuntu bionic-security/universe amd64 Packages [66
9 kB]
default: Get:14 http://us.archive.ubuntu.com/ubuntu bionic-security/universe Translation-en [22
2 kB]
default: Fetched 4,863 kB in 3s (1,475 kB/s)
default: Reading package lists...
default: Building dependency tree...
default:
default: Reading state information...
default: 4 packages can be upgraded. Run 'apt list --upgradable' to see them.
default: + sudo apt install -y htop vim tree
default:
default: WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
default: E: Could not get lock /var/lib/dpkg/lock-frontend - open (11: Resource temporarily unavailable)
default: E: Unable to acquire the dpkg frontend lock (/var/lib/dpkg/lock-frontend), is another process using it?
default: + true
default: ++ ip addr show enp0s8
default: ++ grep 'inet\b'
default: ++ cut -d/ -f1
default: ++ awk '{print $2}'
default: + IP_ADD=192.168.0.48
default: + IP_HOSTS='192.168.0.48 scgdm scgdm.gobii.org'
default: + echo
default: Starting up slapd...
default: + echo 'Starting up slapd...'
default: + echo
default: + docker exec -u root gobii-ldap-node bash -c '
default: service slapd status;
default: service slapd start;
default: sleep 3
default: service slapd status;
default: exit;
default: '
default: * slapd is not running
default: * Starting OpenLDAP slapd
default: ...done.
default: * slapd is running
default: Starting up Haplotool...
default: + echo 'Starting up Haplotool...'
default: + echo
default: + docker exec -u root gobii-haplo-node bash -c '
default: sudo -H -u shiny /usr/bin/shiny-server.sh;
default: exit;
default: '
default: tail:
default: error reading '/var/log/shiny-server/': Is a directory
default: [2020-06-02T15:55:12.783] [INFO] shiny-server - Shiny Server v1.5.9.923 (Node.js v8.11.3)
default: [2020-06-02T15:55:12.789] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
default: [2020-06-02T15:55:13.037] [INFO] shiny-server - Starting listener on http://[::]:3838
default: + true
default: VM IP is: 192.168.0.48
default:
default: Please add the following line to your /etc/hosts file:
default: 192.168.0.48 scgdm scgdm.gobii.org
default: + echo 'VM IP is: 192.168.0.48'
default: + echo
default: + echo 'Please add the following line to your /etc/hosts file: '
default: + echo '192.168.0.48 scgdm scgdm.gobii.org'
default: + echo
default:
default: The instance of scGDM is now deployed and running!
default: Once you have added the above line to your hosts file
default: you can access the Extractor UI @:
default:
default: scgdm.gobii.org:80881/gobii-dev
default:
default: or
default:
default: 192.168.0.48:8081/gobii-dev
default:
default:
default: Deployment completed!
default: + echo '
default: The instance of scGDM is now deployed and running!
default: Once you have added the above line to your hosts file
default: you can access the Extractor UI @:
default:
default: scgdm.gobii.org:80881/gobii-dev
default:
default: or
default:
default: 192.168.0.48:8081/gobii-dev
default: '
default: + echo
default: + echo 'Deployment completed!'
default: + echo
real 3m4.409s
user 0m4.347s
sys 0m3.067s
6.) Toward the end of the output please reference the following sections:
7.) The line specified as:
192.168.0.XXX scgdm scgdm.gobii.org
should be added to your /etc/hosts file for easier access to this VM when using the browser. Otherwise as notated in the second box the links you will access will use the 192.168.0.XXX address notated toward the end of the vagrant up command.
screenshot [ /etc/hosts ]
8.) Access the GOBii Extractor at:
scgdm.gobii.org:8081/gobii-dev
or
192.168.0.XXX:8081/gobii-dev
