Installing Metavisitor with GalaxyKickStart and Ansible¶
Here, a Deployment Machine will install a Metavisitor Galaxy server on Target Machine. Note that Deployment Machine and Target Machine can both be local or remote machines, and that they can be the same machine.
Requirements¶
- On the
Deployment Machine, git and ansible need to be installed. - The
Target Machinehas to be accessible through ssh connection by the user (you) withrootprivileges. This implies that a correct ssh private key file is available on yourDeployment Machine, for instance~/.ssh/id_rsa. This key will be used for secure transactions managed by ansible between theDeployment Machineand theTarget Machine. - see the GalaxyKickStart manual for more detailed informations on how to install appropriate version of Ansible.
Getting the ansible playbook¶
This is done on the Deployment Machine by cloning the GalaxyKickStart (GalaxyKickStart) repository hosted by the ARTbio organization:
In your terminal, type:
and navigate in the GalaxyKickStart folder:GalaxyKickStart makes use of other Ansible roles -- referenced in the requirements_roles.yml file -- that need to be downloaded as part of the installation step:
roles folder.
Adapting the GalaxyKickStart folder to your deployment¶
There are only few things to change in the GalaxyKickStart folder before running ansible.
Adapt the ansible inventory file¶
In the GalaxyKickStart/inventory_files folder, there is a file called the metavisitor.
For deploying Metavisitor, you need to edit this file so that it just contains
[metavisitor]
<ip address> ansible_ssh_user="root" ansible_ssh_private_key_file="<path/to/the/ssh/private/key>"
The <ip address> is the address of the Target Machine. The <path/to/the/ssh/private/key> is the path on the Deployment Machine to your ssh key, to be recognized by the Target Machine.
Thus, a practical exemple of the final content on the inventory file metavisitor is:
where 192.54.201.126 is the ip address of the Target machine and ~/.ssh/id_rsa the path to the private ssh key.
Note that you can also install locally Metavisitor by letting the metavisitor inventory file as is:¶
Adapt the ansible inventory file to an Amazon Web Service (AWS) virtual machine¶
In this specific case, add in the hosts inventory file:
[metavisitor]
192.54.201.126 ansible_ssh_user="ubuntu" ansible_ssh_private_key_file="~/.ssh/aws_private_key.pem"
[aws]
192.54.201.126
aws_private_key.pem is the private ssh key for interacting with aws instances, and the [aws] section will trigger additional actions for accessing the Metavisitor Galaxy instance in the Amazon cloud.
Note that in addition the settings of the security group associated to the AWS instance should be as follows:
Type |Protocole| Port Range | Source | #comment
__________________________________________________________________________________________
HTTP | TCP | 80 | 0.0.0.0/0 | for Galaxy web access
SSH | TCP | 22 | 0.0.0.0/0 | for ssh access to the AWS instance
Custom TCP Rule | TCP | 21 | 0.0.0.0/0 | for FTP upload to Galaxy
Custom TCP Rule | TCP | 49152 - 65534 | 0.0.0.0/0 | for FTP upload to Galaxy
The ports 21 and 49152 - 65534 should be open for FTP uploads to the AWS instance, and port 80 should be open for accessing galaxy.
Adapt the group_vars/all file for persisting data, if needed.¶
In cases where your Target machine has volumes where you wish the Galaxy data to be persisted in, you have to edit the GalaxyKickStart/group_vars/all file, to indicate the path to this volume on the Target machine.
If you don't understand the previous statement, no worries, just don't do anything and skip this step.
For others, find the lines
#persistent data
galaxy_persistent_directory: /export # for IFB it's /root/mydisk, by default, /export
in the GalaxyKickStart/group_vars/all file, and change /export to the path of your persistent volume.
Note that if /export is not changed, nothing will happen and the deployed galaxy server and all associated data files will be in the /home/galaxy/galaxy folder of the Target Machine.
Deploying Metavisitor Galaxy on the Target Machine¶
You are almost done.
Navigate with your terminal to your GalaxyKickStart folder and type the following command to run the ansible playbook for deploying metavisitor Galaxy on the Target Machine:
If everything is ok, you may be asked to authorize the access to the Target Machine by typing yes in the terminal, and you will see ansible orchestrating the serveur deployment on the Target Machine in this terminal.
When the process is finished, you should be able to access the Target Machine by typing its IP address in your web browser.
By default the admin login/password is admin@galaxy.org / admin. You should change the password for safety.
Re-deploying Metavisitor Galaxy on the Target Machine¶
If you are experimented in using ansible, you may customize your Metavisitor Galaxy instance deployed with GalaxyKickStart by editing the content of GalaxyKickStart.
In that case, when your changes are done, just run again the command
When you run the playbook a second time, the process will be much faster, since steps that have already been executed are skipped. Whenever you change a variable (see customizations), you need to run the playbook again.You can put multiple machines in your inventory: a simple way to do this is just copying the line the required number of times with the appropriate ip addresses: