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Merged
gsaudade99 merged 1 commit into from
May 11, 2026
Merged

add el10 support #3

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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ paprikant.beacon
```yaml

script_user: beacon-import
script_dir: /opt/beacon-import/
script_dir: /opt/beacon-import/

galaxy_api_key: 123213hiufho12h31h321
galaxy_api_url: usegalaxy.eu
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2 changes: 1 addition & 1 deletion files/beacon-import.py
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@@ -1,4 +1,4 @@
#!/usr/bin/env python3.9
#!/usr/bin/env python3
"""Pushes genomic variant information from a galaxy to a beacon instance.

Usage:
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10 changes: 5 additions & 5 deletions files/requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
argparse
asyncio
asyncpg
datetime
dataclasses
numpy
typing
git+https://github.com/CSCfi/beacon-python
asyncpg>=0.28.0
numpy
bioblend
cyvcf2

cyvcf2>=0.32.1
aiohttp>=3.8.6
uvloop>=0.17.0
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@domgz domgz May 11, 2026

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argparse<2.0.0
asyncio<5.0.0
DateTime<7.0.0
dataclasses<1.0.0
typing<4.0.0
asyncpg>=0.28.0,<1.0.0
numpy<3.0.0
bioblend<2.0.0
cyvcf2>=0.32.1,<1.0.0
aiohttp>=3.8.6,<4.0.0
uvloop>=0.17.0,<1.0.0

Just in case you think it is useful.

37 changes: 27 additions & 10 deletions tasks/main.yml
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@@ -1,23 +1,22 @@
---
# tasks file for beacon
#

- name: Install python
ansible.builtin.package:
name: "{{ item }}"
state: present
loop:
- python39
- python3
- python3-pip
- python3-setuptools

- python3-devel
- gcc

- name: Install cronie
ansible.builtin.package:
name: cronie
state: present

- name: Ensure script user exists
- name: Ensure script user exists
ansible.builtin.user:
name: "{{ script_user }}"
create_home: true
Expand All @@ -40,24 +39,42 @@
ansible.builtin.package:
name: git
state: present

# this is no mistake

- name: Create virtualenv and bootstrap pip tooling
ansible.builtin.pip:
name:
- pip
- setuptools
- wheel
state: latest
virtualenv: "{{ script_dir }}/venv"
virtualenv_command: /usr/bin/python3 -m venv

- name: Install beacon-python without deps
ansible.builtin.pip:
name: "git+https://github.com/CSCfi/beacon-python"
extra_args: "--no-deps"
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@domgz domgz May 11, 2026

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el10 does not come with python 3.9 and the beacon as some pinned versions that do not work in newer versions of python

I see, therefore --no-deps 👍.

virtualenv: "{{ script_dir }}/venv"
virtualenv_command: /usr/bin/python3 -m venv

- name: Install python deps
ansible.builtin.pip:
requirements: "{{ script_dir }}/requirements.txt"
executable: /usr/bin/pip3.9
virtualenv: "{{ script_dir }}/venv"
virtualenv_command: /usr/bin/python3 -m venv

- name: Create a cronjob for daily executions
- name: Create a cronjob for daily executions
ansible.builtin.cron:
user: "{{ script_user }}"
name: "check dirs"
minute: "0"
hour: "5"
job: "{{ script_dir }}/beacon-import.py -k {{ galaxy_api_key }} -u {{ galaxy_api_url }} rebuild -H {{ beacon_db_host }} -P {{ beacon_db_port }} -U {{beacon_db_user }} -W {{ beacon_db_password }} -N {{ beacon_db_name }} || touch /tmp/job_error"
job: "{{ script_dir }}/venv/bin/python {{ script_dir }}/beacon-import.py -k {{ galaxy_api_key }} -u {{ galaxy_api_url }} rebuild -H {{ beacon_db_host }} -P {{ beacon_db_port }} -U {{ beacon_db_user }} -W {{ beacon_db_password }} -N {{ beacon_db_name }} || touch /tmp/job_error"

- name: Make sure crond is started and enabled
ansible.builtin.systemd:
name: crond
name: crond
state: started
enabled: yes

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