| import logging | |
| from galaxy.jobs.mapper import JobMappingException | |
| log = logging.getLogger(__name__) | |
| DESTINATION_IDS = { | |
| 1 : 'slurm', | |
| 2 : 'slurm-2c' | |
| } | |
| FAILURE_MESSAGE = 'This tool could not be run because of a misconfiguration in the Galaxy job running system, please report this error' |
Adapted from Oslo training
By the end of this tutorial, you should:
Two commonly used [Galaxy][galaxy] server configurations are the use of [uWSGI Zerg Mode][uwsgi-zerg-mode] and [uWSGI Mules][uwsgi-mules] as [Galaxy job handlers][galaxy-scaling]. These features are not easily compatible because Galaxy job handlers rely heavily on having unique server names, and handlers' server names must be persistent across restarts. Because zerg mode results in running two Galaxy servers simultaneously (however briefly), using mules with zerg mode would necessarily mean running mules with overlapping server names.
In a typical Galaxy zerg mode setup, the newly started zergling (B) terminates the old zergling (A) once B is ready to serve requests. Zergling B then continues to serve requests until another zergling (C) is started and terminates B.
It is possible to get both zerg mode and mules working together by configuring zergling B to start without mules, and perform a double zerg dance on each restart:
| #!/usr/bin/env python | |
| import argparse | |
| import sys | |
| import boto3 | |
| from jinja2 import Environment | |
| from s3pypi.exceptions import S3PyPiError | |
| from s3pypi.package import Package |
| Exception in thread database_heartbeart_main.web.6.thread: | |
| Traceback (most recent call last): | |
| File "/cvmfs/test.galaxyproject.org/deps/_conda/envs/_galaxy_/lib/python3.6/threading.py", line 916, in _bootstrap_inner | |
| self.run() | |
| File "/cvmfs/test.galaxyproject.org/deps/_conda/envs/_galaxy_/lib/python3.6/threading.py", line 864, in run | |
| self._target(*self._args, **self._kwargs) | |
| File "lib/galaxy/model/database_heartbeat.py", line 96, in send_database_heartbeat | |
| self.update_watcher_designation() | |
| File "lib/galaxy/model/database_heartbeat.py", line 85, in update_watcher_designation | |
| self.sa_session.flush() |
| <?xml version="1.0"?> | |
| <toolbox> | |
| <!-- | |
| This is Galaxy's integrated tool panel and should be modified directly only for | |
| reordering tools inside a section. Each time Galaxy starts up, this file is | |
| synchronized with the various tool config files: tools, sections and labels | |
| added to one of these files, will be added also here in the appropriate place, | |
| while elements removed from the tool config files will be correspondingly | |
| deleted from this file. | |
| To modify locally managed tools (e.g. from tool_conf.xml) modify that file |
interactivetools_map needs to go in the galaxy section for the Galaxy side<param id="docker_set_user"></param> on destination to run container as root*.interactivetoolentrypoint.interactivetool.example.org where example.org is your Galaxy server.offload-threads causes connnections to fail after 3 connections are made, disabling `offlo
| galaxy.web.framework.decorators ERROR 2019-10-21 13:42:17,701 [p:6121,w:2,m:0] [uWSGIWorker2Core1] Uncaught exception in exposed API method: | |
| Traceback (most recent call last): | |
| File "lib/galaxy/web/framework/decorators.py", line 282, in decorator | |
| rval = func(self, trans, *args, **kwargs) | |
| File "lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py", line 656, in uninstall_repository | |
| errors = irm.uninstall_repository(repository=repository, remove_from_disk=kwd.get('remove_from_disk', True)) | |
| File "lib/tool_shed/galaxy_install/installed_repository_manager.py", line 773, in uninstall_repository | |
| uninstall=remove_from_disk) | |
| File "lib/tool_shed/galaxy_install/tools/tool_panel_manager.py", line 444, in remove_repository_contents | |
| self.app.install_model.context.add(repository) |
| (ansible-latest)nate@weyerbacher% ansible --version | |
| ansible 2.8.5 | |
| config file = /home/nate/ansible/usegalaxy-clone/ansible.cfg | |
| configured module search path = ['/home/nate/.ansible/plugins/modules', '/usr/share/ansible/plugins/modules'] | |
| ansible python module location = /home/nate/.virtualenvs/ansible-latest/lib/python3.7/site-packages/ansible | |
| executable location = /home/nate/.virtualenvs/ansible-latest/bin/ansible | |
| python version = 3.7.3 (default, Apr 3 2019, 05:39:12) [GCC 8.3.0] | |
| (ansible-latest)nate@weyerbacher% cat ansible.cfg | |
| [defaults] | |
| retry_files_enabled = False |
| Friday 27 September 2019 12:51:11 -0400 (0:00:00.004) 0:16:50.574 ****** | |
| =============================================================================== | |
| galaxyproject.galaxy : Run webpack ------------------------------------ 378.58s | |
| galaxyproject.galaxy : Install packages with yarn --------------------- 278.82s | |
| galaxyproject.galaxy : Install Galaxy base dependencies --------------- 187.06s | |
| usegalaxy_cvmfs : Remove node_modules ---------------------------------- 43.87s | |
| galaxyproject.galaxy : Update Galaxy to specified ref ------------------ 20.08s | |
| galaxyproject.galaxy : Install yarn ------------------------------------ 12.77s | |
| usegalaxy_cvmfs : Abort CVMFS transaction ------------------------------ 10.86s | |
| usegalaxy_cvmfs : Fetch Galaxy version ---------------------------------- 9.12s |