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sn07.yml
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sn07.yml
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---
- name: UseGalaxy.eu
hosts: sn07
become: true
become_user: root
vars:
# The full internal name.
hostname: sn07.galaxyproject.eu
# The nginx user needed into the galaxyproject.nginx role
nginx_conf_user: galaxy
# This server has multiple CNAMEs that are important. Additionally it
# provides proxying for many of the other services run by Galaxy Europe.
# These server_names are passed to certbot. They generally should not need
# to be updated unless you add a new domain. They *only* work with the
# route53 provider, so if we want to do usegalaxy.xy, it may require
# refactoring / multiple certbot runs.
#
#
# The best way to expand them is to run the playbook, it will leave a message with the command it would have run (look for `skipped, since /etc/letsencrypt/renewal/usegalaxy.eu.conf exists`)
#
# Then take this command to the command line (root@sn04) and run it with `--expand`. E.g. (DO NOT COPY PASTE (in case the config changes))
#
# $ /opt/certbot/bin/certbot certonly --non-interactive --dns-route53 \
# -m [email protected] --agree-tos -d 'usegalaxy.eu,*.usegalaxy.eu,galaxyproject.eu,*.galaxyproject.eu,*.interactivetoolentrypoint.interactivetool.usegalaxy.eu,*.interactivetoolentrypoint.interactivetool.live.usegalaxy.eu,*.interactivetoolentrypoint.interactivetool.test.usegalaxy.eu' --expand
# Saving debug log to /var/log/letsencrypt/letsencrypt.log
# Credentials found in config file: ~/.aws/config
# ....
# IMPORTANT NOTES:
# - Congratulations! Your certificate and chain have been saved at:
#
# And you're done expanding the certs.
#
# The nginx user needed into the galaxyproject.nginx role
server_names:
- "usegalaxy.eu"
- "*.usegalaxy.eu"
- "galaxyproject.eu"
- "*.galaxyproject.eu"
- "*.interactivetoolentrypoint.interactivetool.usegalaxy.eu"
- "*.interactivetoolentrypoint.interactivetool.live.usegalaxy.eu"
- "*.interactivetoolentrypoint.interactivetool.test.usegalaxy.eu"
vars_files:
- group_vars/tiaas.yml # All of the training infrastructure
- group_vars/custom-sites.yml # Subdomains are listed here
- group_vars/gxconfig.yml # The base galaxy configuration
- group_vars/toolbox.yml # User controlled toolbox
- secret_group_vars/sentry.yml # Sentry SDK init url
- secret_group_vars/aws.yml # AWS creds
- secret_group_vars/pulsar.yml # Pulsar + MQ Connections
- secret_group_vars/oidc.yml # OIDC credentials (ELIXIR, keycloak)
- secret_group_vars/object_store.yml # Object Store credentils (S3 etc ...)
- secret_group_vars/db-main.yml # DB URL + some postgres stuff
- secret_group_vars/file_sources.yml # file_sources_conf.yml creds
- secret_group_vars/all.yml # All of the other assorted secrets...
- secret_group_vars/keys.yml # SSH keys
- templates/galaxy/config/job_conf.yml
collections:
- devsec.hardening
handlers:
- name: Restart Galaxy
shell: |
echo 'Manual web handler restart required' && cd /opt/galaxy/ && source /opt/galaxy/.bashrc && systemctl restart galaxy-handler@* && systemctl restart galaxy-workflow-scheduler@*
pre_tasks:
- name: Install Dependencies
package:
name:
[
"git",
"postgresql",
"python3-psycopg2",
"python3-virtualenv",
"bc",
"python3",
"python3-devel",
]
become: true
post_tasks:
- name: Append some users to the systemd-journal group
user:
name: "{{ item }}"
groups: systemd-journal
append: true
loop:
- "{{ galaxy_user.name }}"
- "telegraf"
- "stats" # special account to retrieve statistics from the server in read-only mode
- name: Set authorized SSH key (galaxy user)
ansible.posix.authorized_key:
user: "{{ galaxy_user.name }}"
state: present
key: "{{ item }}"
loop:
- "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIFH54+qZEBeU5uwIeWWOViLcC509qxoRW6oN0VHRQr4r nate@treehouse"
- "ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBOBINXdjILF6x3WuppXyq6J2a2oSLR6waZ6txgjYJogHdIKPbI0TdReCv4EVxxYRY/NqGpHbjkqfRTsf2VgoU3U= mk@galaxy-mira"
- "ecdsa-sha2-nistp521 AAAAE2VjZHNhLXNoYTItbmlzdHA1MjEAAAAIbmlzdHA1MjEAAACFBACB5Q5blymkTIRSzVzXITOGvBuI7W0L9Ykwfz8LJGPraaGVPiezzFGvjhqwX+EyCqQPt7JprR5mimJRw/JN3nBXWAHjekvmB5FuILkk6m5fOiQJ5QhRMyQ5GfxODAvGbHpTuWHbYJLWD5fhcboKPxlXOWy4xY9kDZVuQvEKisNKYBsFLA== sanjay"
- https://github.com/wm75.keys
- https://github.com/gmauro.keys
- "{{ galaxy_user_public_key }}"
- name: Set authorized SSH key (stats user)
ansible.posix.authorized_key:
user: "stats"
state: present
key: "{{ item }}"
loop:
- "ssh-rsa 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 anup"
- "ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEApcUIRRUHl0wVVXz5GX1QnHSq9+nThIKKH3fYM21LfW1n6gGvC7UiCCaDZQUbejJTq3EITbH3J6/Tji2jGAIJ6Xzn0Jf7sQ1yON/dO/75To32Jdo8YWS7XQeA7lU9heSc7FM5yKIBJN7PrpnYAveCsOE/1kkfUSsBZsqj9yyoFe/tquoVm5Y3nFZfKJv7/gszSVkzNxhHvn+0ccClRLpnFUHjqXgXHIQCm7P/9Lf7unSoYRd9Iefwgp52Lcm6AIncQvz5tdAFD2WciP4J15EFPMTKPdc6tfT5Tis/+/oNfYlsnaIGrbV5Hc2909KiYnvuvqKcrSFloXWzAdXJOxhszw== [email protected]"
- "ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC8/9GdD96Xfc0MavIJQEuNSIrOlaBSYkH4s5RyGhNnc8Al7x3hC7KXt/mcqyNoI1JTvrXp23aDpTr67e3Dnrp6Me7z8nyY9oIy5WHOgwG2ra1Ga8oi89MVgXPhtxvcYnk8hVfuPDmhWkgwS5ILH/7V/1hEKHcS0H7Q0pJp8EGCBDFWrxNfUWqJJuVcXb11CMnaSJX/VhD+S4g4rG01lMr696+k8eKs9y2sq9JpuUD1TNN16RYu1uVlVz8nhIPbEBsnFeKV+EYKLcSRQnjDTNjWqZHHM9NMWfK3wGvr5pfla158ZdsYQTmQtcchTsEoB+7eAQaER3XsEtuo8yQj4zbL videmp@work"
- "ssh-rsa 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 ubuntu@pavan-dedicated-vm"
- "ssh-rsa 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 laptop@freiburg"
- "ssh-rsa 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 david"
- "ecdsa-sha2-nistp521 AAAAE2VjZHNhLXNoYTItbmlzdHA1MjEAAAAIbmlzdHA1MjEAAACFBAA6oD5Ps9h6pKokzaAcCI6R08CKm2aSVv86h/O2HTEQkzeJq/Uvu4gbrONAM0FK5R693mHggIwaROKf1Z1+q4YNtACtYjV1c+6a9lcrGMM31y5RzO6mAW+rHNEXgZ1n3wqDcBQhSXhSekSen0R2QKwvmB7xeP4XX9qE10azZuafIFU9hQ== sanjay"
- "ssh-rsa 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 bebatut@bebatut-ThinkPad-T14-Gen-1"
- "ecdsa-sha2-nistp521 AAAAE2VjZHNhLXNoYTItbmlzdHA1MjEAAAAIbmlzdHA1MjEAAACFBADKblzzPBc3+dEfFvhJQHsHGkFFN6ORjfXo71P1OutwcKEMCIcNkZKJHhYkLLrfTDN5JJ5tK2L5AaSxdwETofwm4AG1xv3LuoYsXC6e3sjKi09BVmzef520pIMW+rvL+hESwSazZaUAC0wDcH4aNDTonZYcAY87rpMX7pNMkNPJvWilUA== mira"
- "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIFH54+qZEBeU5uwIeWWOViLcC509qxoRW6oN0VHRQr4r nate"
- "ecdsa-sha2-nistp521 AAAAE2VjZHNhLXNoYTItbmlzdHA1MjEAAAAIbmlzdHA1MjEAAACFBABRaLHL8mgW86rbtdUh6TY4rs7/la8hAGeSQ3jBF7LMwYZnbS32YDMYvDq3KgNu5WqSMFvkxNm3vfTAbd8CXBfakwDBFBaD9kO0b2t4/p4VoFUsd3B2OvmTR7Bsg7OxTGJJ7aUP/SzTg+Z4NzsmHwQ9h31gfI7n/buZD4S1edQke19Y6w== [email protected]"
# Add SELinux policy for nginx to interact with the gunicorn socket
- name: Check if nginx-gunicorn selinux policy is installed
command: semodule --list=full | grep -q nginx_gunicorn_selinux
register: nginx_gunicorn_selinux_policy
failed_when: nginx_gunicorn_selinux_policy.rc > 1
- name: Add SELinux policy for nginx to interact with the gunicorn socket
when: nginx_gunicorn_selinux_policy.rc == 1
block:
- name: Copy nginx-gunicorn selinux type enforcement file
copy:
src: "files/galaxy/config/nginx_gunicorn_selinux.te"
dest: "/tmp/nginx_gunicorn_selinux.te"
- name: Compile nginx-gunicorn selinux module
command: "checkmodule -M -m -o /tmp/nginx_gunicorn_selinux.mod /tmp/nginx_gunicorn_selinux.te"
- name: Compile nginx-gunicorn selinux policy package
command: "semodule_package -o /tmp/nginx_gunicorn_selinux.pp -m /tmp/nginx_gunicorn_selinux.mod"
- name: Install nginx-gunicorn selinux policy package
command: "semodule -i /tmp/nginx_gunicorn_selinux.pp"
- name: Clean up nginx-gunicorn selinux policy files
file:
path: "{{ item }}"
state: absent
with_items:
- "/tmp/nginx_gunicorn_selinux.te"
- "/tmp/nginx_gunicorn_selinux.mod"
- "/tmp/nginx_gunicorn_selinux.pp"
# Add http and https to the current firewall zone
- name: Add http and https services to the current firewall zone
firewalld:
service: "{{ item }}"
immediate: true
permanent: true
state: enabled
with_items:
- http
- https
- name: Change compliance.log file ownership to the galaxy user
file:
path: "{{ galaxy_server_dir }}/compliance.log"
owner: galaxy
group: root
mode: 0644
roles:
## Starting configuration of the operating system
- role: usegalaxy_eu.handy.os_setup
vars:
enable_hostname: true
enable_powertools: true # geerlingguy.repo-epel role doesn't enable PowerTools repository
enable_remap_user: true
enable_exclude_packages: true
enable_pam_limits: true # Prevent out of control processes
enable_install_software: true # Some extra admin tools (*top, vim, etc)
- geerlingguy.repo-epel # Install EPEL repository
## Istall miniconda, create a _galaxy_ environment and install Packages
## Galaxy will use the virtualenv from this conda environment (see
## galaxy_virtualenv_command) in the group_vars/sn07.yml
- role: galaxyproject.miniconda
vars:
miniconda_prefix: "{{ conda_prefix }}"
galaxy_conda_create_env: true
galaxy_conda_env_packages:
- python=3.8
- pip
- virtualenv
- usegalaxy-eu.autoupdates # keep all of our packages up to date
- influxdata.chrony # Keep our time in sync.
## Filesystems
- usegalaxy-eu.autofs # Setup the mount points which will be needed later
- galaxyproject.cvmfs # Galaxy datasets
## Monitoring
# this should be unique, because it sends data to about the cluster to influxDB
#- hxr.monitor-cluster
- hxr.monitor-email
- hxr.monitor-galaxy-journalctl
# - usegalaxy-eu.monitor-disk-access-time merged with usegalaxy-eu.monitoring
# uses the nfsstat command only
- usegalaxy-eu.monitoring
# Setup Galaxy user
- role: galaxyproject.galaxy
vars:
galaxy_create_user: true
galaxy_manage_clone: false
galaxy_manage_download: false
galaxy_manage_existing: true
galaxy_manage_paths: true
galaxy_manage_static_setup: false
galaxy_manage_mutable_setup: false
galaxy_manage_database: false
galaxy_fetch_dependencies: false
galaxy_build_client: false
# The bashrc needs to be created for several later features.
- usegalaxy-eu.bashrc
# HTCondor Cluster setup
# - usegalaxy_eu.htcondor
# Misc.
- role: hxr.galaxy-nonreproducible-tools
become: true
become_user: galaxy
- usegalaxy-eu.dynmotd # nicer MOTD/welcome message
# - usegalaxy-eu.rsync-to-nfs # sync codebase to NFS
- role: usegalaxy-eu.webhooks # Clone webhook repository
become: true
become_user: galaxy
- role: usegalaxy-eu.tours # Clone tour repository
become: true
become_user: galaxy
## SSL / Security
# https://en.wikipedia.org/wiki/Trust_on_first_use
- ssh-host-sign # Sign the server host key to prevent TOFU for SSH
- hxr.aws-cli # Setup the AWS client that will be needed for route53 authentication of certbot. MUST come before nginx role
## GALAXY
- hxr.postgres-connection
- galaxyproject.gxadmin
- usegalaxy_eu.ansible_nginx_upload_module
- usegalaxy-eu.nginx
# TODO move under monitoring + telegraf.
# Role that creates a cron to gather galaxy stats, neets to run only on one node
#- usegalaxy-eu.galaxy-slurp
- usegalaxy-eu.gapars-galaxy
# The REAL galaxy role
- role: galaxyproject.galaxy
vars:
galaxy_create_user: true
galaxy_manage_clone: true
galaxy_manage_download: false
galaxy_manage_existing: false
galaxy_manage_static_setup: true
galaxy_manage_mutable_setup: true
galaxy_manage_database: true
galaxy_fetch_dependencies: true
galaxy_build_client: true
- role: galaxyproject.tiaas2
vars:
tiaas_virtualenv_command: "{{ galaxy_virtualenv_command }}"
## Extras!
- usegalaxy-eu.fix-galaxy-server-dir # Fix details into the galaxy server dirs
- hxr.install-to-venv # Some extra packages our site needs.
- usegalaxy_eu.galaxy_systemd # Manage the Galaxy processes with SystemD
- usegalaxy-eu.update-hosts # Update hosts list
- usegalaxy_eu.gie_proxy # Setup the NodeJS proxy for GxIT
- usegalaxy-eu.subdomain-themes # Custom subdomain themes
# This is mixed: schedules cron to submit condor jobs that clean up dirs
# also cleans up docker and 'gxadmin cleanup 60'
#- usegalaxy_eu.fs_maintenance # Filesystems maintenance
- usegalaxy-eu.error-pages # Copy the NGINX error pages
# Needs to run only on one machine, and only if condor is actually available
#- usegalaxy-eu.htcondor_release # Condor release held jobs increasing memory
# Various ugly fixes
- usegalaxy-eu.fix-stuck-handlers # Restart handlers to prevent several classes of issues
# first one sets the logrotate.d config for galaxy, second vacuums galaxy-xxx@* at midnight
- usegalaxy-eu.logrotate # Rotate galaxy logs on headnodes
- usegalaxy-eu.log-cleaner # do not retain journalctl logs, they are unnecessary/risky under GDPR
#- usegalaxy-eu.fix-ancient-ftp-data # Remove FTP data older than 3 months, create FTP user directories
# Some of our 'cleanups' also generate telegraf format so this goes at end.
# 25.11.2022: Moved here becuase the galaxy-procstat role fails
# as it is not able to find the /etc/telegraf/telegraf.d/ directory
- dj-wasabi.telegraf
# This one creates telegraf plugins for the galaxy-xxxx@* services (now with gunicorn!)
- usegalaxy-eu.galaxy-procstat # Some custom telegraf monitoring that's templated
# This can be moved to maintenance machine (gxadmin mutate ...)
#- usegalaxy-eu.fix-user-quotas # Automatically attribute ELIXIR quota to ELIXIR AAI user on a regular basis
# - dev-sec.os-hardening
- ssh_hardening #dev-sec.hardening collection
## Setup docker commented on 11/30/2022, remove if everything works
#- geerlingguy.docker
- usegalaxy_eu.tpv_auto_lint