mvdbeek

workflows:
- trs_id: '#workflow/github.com/iwc-workflows/assembly-with-flye/main/versions/v0.2'
  workflow_categories:
  - ASSEMBLY
  workflow_name: Genome assembly with Flye
  workflow_description: Assemble long reads with Flye, then view assembly statistics
    and assembly graph
  ploidy: any
  parameters:
    Input sequence reads:

mvdbeek

[
  {
    "version": 1.2,
    "workflows": [
      {
        "name": "main",
        "subclass": "Galaxy",
        "publish": true,
        "primaryDescriptorPath": "/Mass_spectrometry__LC-MS_preprocessing_with_XCMS.ga",
        "testParameterFiles": [

mvdbeek

{"$defs": {"CollectionAttributes": {"additionalProperties": false, "properties": {"collection_type": {"anyOf": [{"type": "string"}, {"type": "null"}], "default": null, "title": "Collection Type"}}, "title": "CollectionAttributes", "type": "object"}, "OutputCompareType": {"enum": ["diff", "re_match", "sim_size", "re_match_multiline", "contains", "image_diff"], "title": "OutputCompareType", "type": "string"}, "RootModel_List_Union_Annotated_Union_has_line_model__has_line_matching_model__has_n_lines_model__has_text_model__has_text_matching_model__not_has_text_model__has_n_columns_model__attribute_is_model__attribute_matches_model__element_text_model__element_text_is_model__element_text_matches_model__has_element_with_path_model__has_n_elements_with_path_model__is_valid_xml_model__xml_element_model__has_json_property_with_text_model__has_json_property_with_value_model__has_h5_attribute_model__has_h5_keys_model__has_archive_member_model__has_size_model__has_image_center_of_mass_model__has_image_channels_model__has

mvdbeek

changed: [cvmfs0-psu1.galaxyproject.org] => (item=client)
failed: [cvmfs0-psu1.galaxyproject.org] (item=plugins) => {"ansible_loop_var": "item", "changed": true, "cmd": ["yarn", "run", "gulp", "plugins"], "delta": "0:09:31.824149", "end": "2024-06-21 15:56:11.744263", "item": "plugins", "msg": "non-zero return code", "rc": 1, "start": "2024-06-21 15:46:39.920114", "stderr": "warning \" > [email protected]\" has incorrect peer dependency \"webpack@^3.1.0\".\nwarning \"@h5web/app > @h5web/lib > [email protected]\" has incorrect peer dependency \"react@^16.3.0 || ^17.0.0\".\nwarning \"@h5web/app > @react-three/fiber > [email protected]\" has incorrect peer dependency \"react@^17.0.2\".\nBrowserslist: caniuse-lite is outdated. Please run:\n  npx update-browserslist-db@latest\n  Why you should do it regularly: https://github.com/browserslist/update-db#readme\nBrowserslist: caniuse-lite is outdated. Please run:\n  npx update-browserslist-db@latest\n  Why you should do it regularly: h

mvdbeek

import json
import subprocess
import time

from requests import Session

from galaxy.tool_util.deps.mulled.util import quay_versions
from galaxy.tool_util.deps.mulled.util import _get_namespace

mvdbeek

# Run from galaxy root with PYTHONPATH=lib GALAXY_CONFIG_FILE=config/galaxy.yml  python example.py
import os

from scripts.db_shell import config
from galaxy.celery import get_galaxy_app
from galaxy.managers.api_keys import ApiKeyManager

EMAIL = "[email protected]"

os.environ["GALAXY_CONFIG_FILE"] = os.environ.get("GALAXY_CONFIG_FILE", config["config_file"])

mvdbeek

BEGIN;

-- Clean up pgcleanup table
DELETE FROM cleanup_event_history_association WHERE cleanup_event_history_association.history_id IN (SELECT id FROM history WHERE history.user_id is null AND history.hid_counter = 1 ORDER BY history.update_time LIMIT 100);
-- Clean up audit table
DELETE FROM history_audit WHERE history_audit.history_id IN (select id from history where history.user_id is null and history.hid_counter = 1 ORDER BY history.update_time LIMIT 100);
-- Cleanup galaxy_session_to_history
DELETE FROM galaxy_session_to_history WHERE galaxy_session_to_history.session_id IN (SELECT galaxy_session.id FROM galaxy_session WHERE galaxy_session.current_history_id IN (SELECT history.id FROM history WHERE history.user_id is null AND history.hid_counter = 1 ORDER BY history.update_time LIMIT 100));
-- Clean up galaxy_session
DELETE FROM galaxy_session WHERE galaxy_session.current_history_id IN (select id from history where history.user_id is null AND history.hid_counter = 1 ORDER BY history.update_time LIMIT 10

mvdbeek

Hmm, those tests are passing, but if you look at the logs it appears that some functionality is actually broken ?

```
================================================================ test session starts =================================================================
platform darwin -- Python 3.11.7, pytest-7.4.4, pluggy-1.4.0 -- /Users/mvandenb/src/galaxy/.venv/bin/python3.11
cachedir: .pytest_cache
metadata: {'Python': '3.11.7', 'Platform': 'macOS-14.1.1-arm64-arm-64bit', 'Packages': {'pytest': '7.4.4', 'pluggy': '1.4.0'}, 'Plugins': {'cwltest': '2.4.20240129145612', 'asyncio': '0.23.5', 'postgresql': '5.1.0', 'instafail': '0.5.0', 'shard': '0.1.2', 'html': '4.1.1', 'json-report': '1.5.0', 'pytest_httpserver': '1.0.9', 'metadata': '3.1.1', 'cov': '4.1.0', 'playwright': '0.4.4', 'mock': '3.12.0', 'base-url': '2.1.0', 'anyio': '4.2.0', 'celery': '0.0.0'}, 'Base URL': ''}
rootdir: /Users/mvandenb/src/galaxy
configfile: pytest.ini
plugins: cwltest-2.4.20240129145612, asyncio-0.23.5, postgresql-5.1.0, instafai

mvdbeek

❯ python setup.py bdist_wheel
requirement found install_requires requests<=2.31.0,>=2.25.1
requirement found install_requires urllib3~=1.26.18
requirement found install_requires dogpile.cache~=1.2.2
requirement found install_requires tabulate~=0.9.0
requirement found install_requires jsonschema~=4.20.0
requirement found install_requires paramiko~=3.4.0
requirement found kerberos kerberos~=1.3.1
requirement found kerberos pykerberos~=1.2.4
requirement found kerberos requests-kerberos>=0.14.0

mvdbeek

# VGP Kmer profiling and mitogenome report

Time workflow was run:

```galaxy
invocation_time()
```


## GenomeScope results