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 ]
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PrerequisitesMinimum System Hardware Recommendations: CPU: 4 Cores Memory (RAM): 8 GB Storage: 100 GB ( At deployment time the virtual machine will use 23 GB but has a dynamic disk that can use up to 100 GB ) Image Size: 11.8 GB ( The image that is downloaded from the vagrant repository. Please make sure you have a constant network connection to download this image. )
The requirements specified as the MINIMUM hardware requirements suggested for this system. The deployment is defaulted with 2 vcpus & 2GB RAM. |
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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.
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Please verify you have completed the above requirements fully before attempting to deploy scGDM on your local machine.
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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.
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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 $2}'
default: + IP_ADD=192.168.0.48
default: + IP_HOSTS='192.168.0.48 scgdm scgdm.gobii.org'
default: + echo
default: Starting up slapd...
default: + echo 'Starting up slapd...'
default: + echo
default: + docker exec -u root gobii-ldap-node bash -c '
default: service slapd status;
default: service slapd start;
default: sleep 3
default: service slapd status;
default: exit;
default: '
default: * slapd is not running
default: * Starting OpenLDAP slapd
default: ...done.
default: * slapd is running
default: Starting up Haplotool...
default: + echo 'Starting up Haplotool...'
default: + echo
default: + docker exec -u root gobii-haplo-node bash -c '
default: sudo -H -u shiny /usr/bin/shiny-server.sh;
default: exit;
default: '
default: tail:
default: error reading '/var/log/shiny-server/': Is a directory
default: [2020-06-02T15:55:12.783] [INFO] shiny-server - Shiny Server v1.5.9.923 (Node.js v8.11.3)
default: [2020-06-02T15:55:12.789] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
default: [2020-06-02T15:55:13.037] [INFO] shiny-server - Starting listener on http://[::]:3838
default: + true
default: Restarting Tomcat Webservice...
default: + echo 'Restarting Tomcat Webservice...'
default: + echo
default: + docker exec -i -u gadm gobii-web-node bash -c '
default: /usr/local/tomcat/bin/shutdown.sh; default: sleep 3;
default: /usr/local/tomcat/bin/startup.sh;
default: sleep 3
default: exit;
default: '
default: NOTE: Picked up JDK_JAVA_OPTIONS: --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java$
rmi/sun.rmi.transport=ALL-UNNAMED
default: Jun 02, 2020 4:22:59 PM org.apache.catalina.startup.Catalina stopServer
default: SEVERE: Could not contact [localhost:8005] (base port [8005] and offset [0]). Tomcat may not be running.
default: Jun 02, 2020 4:22:59 PM org.apache.catalina.startup.Catalina stopServer
default: SEVERE: Error stopping Catalina
default: java.net.ConnectException: Connection refused
default: at java.base/sun.nio.ch.Net.connect0(Native Method)
default: at java.base/sun.nio.ch.Net.connect(Net.java:493)
default: at java.base/sun.nio.ch.Net.connect(Net.java:482)
default: at java.base/sun.nio.ch.NioSocketImpl.connect(NioSocketImpl.java:588)
default: at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:339)
default: at java.base/java.net.Socket.connect(Socket.java:603)
default: at java.base/java.net.Socket.connect(Socket.java:552)
default: at java.base/java.net.Socket.<init>(Socket.java:475)
default: at java.base/java.net.Socket.<init>(Socket.java:249)
default: at org.apache.catalina.startup.Catalina.stopServer(Catalina.java:513)
default: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
default: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
default: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
default: at java.base/java.lang.reflect.Method.invoke(Method.java:567)
default: at org.apache.catalina.startup.Bootstrap.stopServer(Bootstrap.java:390)
default: at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:480)
default: Tomcat started.
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 |
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