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Self-Contained GOBii Data Manager (scGDM)

Self-Contained GOBii Data Manager (scGDM)

Owned by Roy Petrie
Last updated: Jun 02, 2020
6 min read

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 ]

Prerequisites

Minimum 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.

Software Requirements

Virtualbox [ Download ]

This is the virtual software used to host the virtual machine.

  • Ubuntu Version: 5.2.34_Ubuntu r133883

Vagrant [ Download ]

This software uses an image repository for the automated Virtual Machine creation.

  • Ubuntu Version: Vagrant 2.0.2

Git [ Windows Download ]

This is the software used to clone the repository.

  • Ubuntu version: git version 2.17.1

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/

cd 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:

vagrant up

At this point vagrant will start a download of the image within the vagrant cloud repo.

This process can take some time to complete depending on network speeds!

The output for this command should show the following:

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

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.

8.) Access the GOBii Extractor at:

scgdm.gobii.org:8081/gobii-dev

or

192.168.0.XXX:8081/gobii-dev

 

 

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