add el10 support

Author: gsaudade99

README.md

@@ -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

files/beacon-import.py

@@ -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:

files/requirements.txt

@@ -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

tasks/main.yml

@@ -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
@@ -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"
+    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