Galaxy (galaxyproject) Instructions

This documents aims for who has no or little experience Ansible or Saltstack (pick one). May not be complete at this time of writing.**

These documents includes -

• Instruction/Notes to deploy Galaxy using SaltStack from https://github.com/rabb13/saltstack-galaxy.
• Notes to deploy Galaxy using Ansible from https://github.com/rabb13/ansible-galaxy.
• Script to fix tools which are currently broken when you try install from tool shed.
• Script to Download and Update datamanager (.loc) files
• Install annovar (Not including the tool itself)

Version compatiblity:

Galaxy:

Tested - v17.09 & 18.01** Compatiblity - 17. +

OS:

Tested: Ubuntu 16.04 Compatbilty : Ubuntu 16.04 + , Redhat/CentOS 7 + (Maybe Most major release with systemd)

Saltstask:

Tested: 2016.11 Compatiblity: 2016.11 _

Ansible:

Tested: 2.4.0 Compatiblity: 2.4 +

Deploying Galaxy using saltstack-galaxy _

• Install salt minion : Follow instruction based on your distribution .
• Standalone Salt Minion setup : Follow instruction here .
• example configuration of "/etc/salt/minion"

#----------------------
master_type: "disable"
file_client: local
file_roots:
  base:
    - /srv/salt
pillar_roots:
  base:
    - /srv/pillar
#----------------------

• Copy the dirctory saltstack/galaxy to /srv/salt
• Create a file "/srv/pillar/top.sls" and Enter the configuration based on pilalr.example <https://github.com/rabb13/saltstack-galaxy/blob/master/pillar.example>

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Deploying Galaxy using ansible-galaxy _

• Install Ansible : Instructions here- .
• In this example we will use local host with default ansible config.
• Copy the contents of ansible-galaxy to "/etc/asible/roles/galaxy" (create directory i you need to)
• Give your localhost a name: add a line "galaxy-local ansible_connection=local"
• Create a playbook for galaxy-local, e.g. "/etc/ansible/galaxy-local.yml'
• example config:

- hosts:

- galaxy-local

roles:

- postgresql # Only if you want to use postgres

- nginx # only if you want to use nginx

- galaxy

• Create vars file for this host here- "/etc/ansible/hosst_vars/galaxy-local.yml" and Enter the Vars exlained here

Tools fixer - "bx-python"

Reason: currently the galaxy tool depndeny "package_bx_python_0_7" is broken. Fix:

• Download the script galaxy_fix_bx-python.sh .
• open it with an editor, make sure all the variables are set correctly
• make it executable: chmod +x galaxy_fix_bx-python.sh
• run it: ./galaxy_fix_bx-python.sh

DataManager Update

Note: This will update Galaxy datamanager list automatically Instrcution:

• Download the script : galaxy_datamanager_update.sh
• open it with an editor, make sure all the variables and loc file list are updated
• make it executable: chmod +x galaxy_datamanager_update.sh
• run it: ./galaxy_datamanager_update.sh

TO BE CONTINUED

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