In order to specify repeititve uWSGI options, the value of the option should be a list. An Ansible role for installing and managing Galaxy servers. Has email templated notification (can also be used to just send info without deleting). custom restart handler, you can use the "listen" option to the handler as explained in the Jul 2012 - Oct 20164 years 4 months. -l LOG_DIR, --log-dir LOG_DIR Are you sure you want to create this branch? The role can now manage the Galaxy service using gravity. You should be doing this anyway. This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. Using Vagrant box generic/centos7 this role fails with message, The file /var/lib/pgsql/9.6/initdb.log has the following message. The website and infrastructure is licensed under MIT. ok ! Instantly share code, notes, and snippets. See the rank of galaxyproject/ansible-postgresql on GitHub Ranking. 'It was Ben that found it' v 'It was clear that Ben found it'. Use Git or checkout with SVN using the web URL. Mark datasets as deleted that are older than specified cutoff. The Galaxy Training Network Check out our Tutorial. Note that the defaults are not merged with your config, so you should fully define the Using Vagrant box generic/centos7 this role fails with message TASK [galaxyproject.postgresql : Initialize database Where communities thrive. What happens if you run the command manually on the target host with the same user as your playbook ? In C, why limit || and && to evaluate to booleans? To access Cloudera Manager on your cluster: . Requirements. DEPRECATED: Comma-separated sequence of actions uWSGI's internal YAML parser expects YAML in an non-standards-conforming syntax: Note that regardless of which galaxy_uwsgi_yaml_parser you use, galaxy_config.uwsgi should be written in real Ansible fails with runuser: command not found, https://docs.ansible.com/ansible/latest/user_guide/playbooks_environment.html, Making location easier for developers with new data primitives, Stop requiring only one assertion per unit test: Multiple assertions are fine, Mobile app infrastructure being decommissioned. galaxyproject/ansible-galaxy. This option In Galaxy, when something is marked deleted, it still exists with a deleted flag. In order to simplify configuration, Create a Project in a PostgreSQL Database. Either the root-dir or opt layout is recommended for new Galaxy deployments. option/value hashes. Also support systemd user, Quotes are not supported: all values are read as strings, Multiple overlapping keys are used to specify multiple instances of an option, Despite appearing to be a YAML dictionary, the order of the dictionary keys in the config is preserved, The remaining list members are the option/values in the control block, Galaxy code (clone) is "clean": no configs or mutable data live underneath the clone, Galaxy code and static configs are privilege separated: not owned/writeable by the user that runs Galaxy, Configuration files are not world-readable, PostgreSQL is used as the backing database, The 18.01+ style YAML configuration is used, When the Galaxy code or configs are updated by Ansible, Galaxy will be restarted using. Use the dry run option to verify what datasets you are about to affect. Set PostgreSQL work_mem for this connection The fancy thing is very fancy, but lacks restore instructions and I'm not entirely sure what the restore process is, just replace the directory? Log in to https://your-utility-node-1:7183 , where your-utility-node is the public or private IP address for . Second attempt at solving post-19.09 mutable file setup, Set an arbitrarily long width for uwsgi YAML line lengths (I highly, Update minimum (and test) version of Ansible to 2.10, Added check vs galaxy version before writing uwsgi section to galaxy.yml, Make sure tool data is in the mutable data dir, Support Running Galaxy 22.01+ with Gravity. In the latter case, order is preserved, and allows for use of uWSGI's configuration To subscribe to this RSS feed, copy and paste this URL into your RSS reader. This -w WORK_MEM, --work-mem WORK_MEM The Galaxy Project. => { Does squeezing out liquid from shredded potatoes significantly reduce cook time? -h, --help show this help message and exit A tag already exists with the provided branch name. I'm noticing my backups stopped a while back. Jump start your automation project with great content from the Ansible community Ansible), Back up the parts of Galaxy that can't be recreated. By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. why is there always an auto-save file in the directory where the file I am editing? users have no permissions). Which layout you choose affects the required variables. Galaxy config file (defaults to, else to ./config/galaxy.ini if that exists). Codebase contains scripts that can assist with cleaning up and reclaiming space. delete_exported_histories, delete_inactive_users, Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. At first it seems that the config file for galaxy is not being found. An Ansible role for managing a Galaxy server. aware that your configuration file permissions may change as of 0.9.18 and later. the same play as this role: If your git executable is not on $PATH, you can specify its location with the git_executable variable. Dcouvrez en images les prvisions mto compltes du 18 octobre 2022 Paris et en le-de-France sur BFM Paris le-de-France, la premire chane d'information de la rgion parisienne. Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational . current working directory: /home/ trinity /galaxy/ server . Options below that control individual file or subdirectory placement can still override defaults set by the layout. service will be automatically started and configured to start when your system boots. Created . In the latter case, order is preserved, and allows for use of uWSGI's configuration logic, for which the order matters. service with the systemctl utility as the root user or with sudo: You can use systemd user mode if you do not have root privileges on your system by setting galaxy_systemd_root to I don't want to change the external role galaxyproject.postgresql of course. I am trying to provision a PostgreSQL server using role galaxyproject.postgresql. How can I make runuser command available to Ansible? Not the answer you're looking for? In older versions, the role did not control the permissions of configuration files, so be The galaxy home is /home/trinity/galaxy and is in root config. The documentation says this: false. Originally posted by @hexylena in #30 (comment). So the problem seems to be that /sbin is not on the PATH when Ansible runs on target nodes. Reason for use of accusative in this phrase? Why don't we know exactly where the Chinese rocket will fall? optional arguments: Add --user to the systemctl commands above to interact with systemd in user mode: Install Galaxy on your local system with all the default options: If your Ansible version >= 2.10.4, then when you run ansible-playbook playbook.yml you should supply an extra argument -u $USER, otherwise you will get an error. In case of an incident do not rush even when pressure is piling. The fancy thing is very fancy, but lacks restore instructions and I'm not entirely sure what the restore process is, just replace the directory? user if deemed necessary. Making statements based on opinion; back them up with references or personal experience. writefifo:/srv/galaxy/var/zerg-run.fifo 2q, writefifo:/srv/galaxy/var/zerg-new.fifo 1, spinningfifo:/srv/galaxy/var/zerg-new.fifo 1, /static/style={{ galaxy_server_dir }}/static/style/blue, galaxy.webapps.galaxy.buildapp:uwsgi_app(), ['git', 'python-psycopg2', 'python-virtualenv']. Connect and share knowledge within a single location that is structured and easy to search. By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. YAML because Ansible parses it with libyaml, which does not support the uWSGI internal parser's invalid syntax. Why is SQL Server setup recommending MAXDOP 8 here? Copyright IssueAntenna. Many variables control where specific files are placed and where Galaxy writes data. QGIS pan map in layout, simultaneously with items on top. Galaxy. with the virtualenv executable and corresponding galaxy_virtualenv_command variable. All Rights Reserved. ['git', 'make', 'python-psycopg2', 'python-virtualenv'], chown -R www-data:galaxy /export/galaxy/database/tmp/nginx_upload_store, /export/galaxy/database/job_working_directory, /export/galaxy/database/tmp/nginx_upload_store, new_user_dataset_access_role_default_private, galaxy/static/style={{ galaxy_server_dir }}/static/style/blue, galaxy/static={{ galaxy_server_dir }}/static, /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app(), environment=HOME={{ galaxy_mutable_data_dir }},VIRTUAL_ENV={{ galaxy_venv_dir }},PATH={{ galaxy_venv_dir }}/bin:%(ENV_PATH)s. You signed in with another tab or window. The Galaxy Project We provide the leadership and resources that the youth need to be a catalyst for change in our community. Dcouvrez en images les prvisions mto compltes du 31 octobre 2022 Paris et en le-de-France sur BFM Paris le-de-France, la premire chane d'information de la rgion parisienne. this role). Overriding this behavior is discussed in the defaults file. Only perform action(s) on objects that have not been Why can we add/substract/cross out chemical equations for Hess law? Asking for help, clarification, or responding to other answers. Is there something like Retr0bright but already made and trustworthy? -s SEQUENCE, --sequence SEQUENCE It can aggravate users. -U, --no-update-time Don't set update_time on updated objects Consider running a recovery drill pretending that e.g. Can only delete (or purge) dataset when all associations pointing at it have been marked deleted. The role needs to perform tasks as different users depending on which features you have enabled and how you are -c CONFIG_FILE, --config-file CONFIG_FILE, --config CONFIG_FILE logic, for which the order matters. Clone with Git or checkout with SVN using the repositorys web address. To learn more, see our tips on writing great answers. When specifying control logic such as if-* and for, the value of the option is a list where: For example, to use if-exists as is commonly done for uWSGI Zerg Mode, use: The role converts this to the following galaxy.yml contents: Several variables control which functions this role will perform (all default to yes except where noted): Options for configuring Galaxy and controlling which version is installed. Stack Overflow for Teams is moving to its own domain! In the former case, the options will be written to galaxy.yml in sorted order, since hashes do not maintain order. To override the default uWSGI configuration, place your uWSGI options under the uwsgi key in the galaxy_config Join over 1.5M+ people Join over 100K+ communities Free without limits Create your own community Explore more communities purge_historyless_hdas, update_hda_purged_flag Additionally, support for the galaxy_restart_handler_name variable has been removed. When the migration is complete, you will access your Teams at stackoverflowteams.com, and they will no longer appear in the left sidebar on stackoverflow.com. Arguably a distribution problem (looking at you ubuntu) but, the backup script stopped working in Dec 2021. https://github.com/xolox/python-rotate-backups, That's a pretty comprehensive list of steps, could probs do that in gh actions. When you yum update sometimes it installs a version of psycopg2 from the wrong version's repo. Thanks for contributing an answer to Stack Overflow! uwsgi section if you choose to set it. Does the Fog Cloud spell work in conjunction with the Blind Fighting fighting style the way I think it does? The value of galaxy_config.uwsgi can be either a hash (dictionary) of option/value pairs, or a list of one-item option/value hashes. By default, the role will use become (i.e. One of the important admimn tasks is to keep an eye on the storage consumption. These can easily be installed via a pre-task in connecting to the target host. You can control the Galaxy purge_hdas_of_purged_histories, Work fast with our official CLI. Any plan to fix this? sudo) to perform tasks as the appropriate I am trying to provision a PostgreSQL server using role galaxyproject.postgresql. erroroutput. For additional information about less commonly used variables, see This dictionary explained below. Getting started with this module? Use configuration management (e.g. Use your systems recommended way to back up galaxys database. The Galaxy Project empowers our youth, and through them, their families and our community as a whole. Some optional configuration files commonly used in production Galaxy servers can be configured from variables: As of Galaxy 21.05 the sample configuration files for these features are in XML, but YAML is supported like so: Options for controlling where certain Galaxy components are placed on the filesystem. There was a problem preparing your codespace, please try again. delete_userless_histories, purge_datasets, This role works with both Debian and RedHat based systems, and provides backup scripts for PostgreSQL Continuous Archiving and Point-in-Time Recovery. One of the included scripts can send templated email to the affected users. postgresql_pgdata: Only set this if you have changed the $PGDATA directory from the package default. View markdown source on GitHub Server Maintenance and Backups Contributors Nate Coraor, Bjrn Grning, Simon Gladman, Helena Rasche Questions Every instance should have a data rention policy defined and shared with users. For the moment, I'm jsut trying to make it work out of the box (jsut after molecule init and set tests platforms) but I'm stuck with this step "check pgdg repo package" :/ If I'll be able to find a solution, I'll share it for sure ! provides researchers with online training materials, connects them with local trainers, and helps promoting open data analysis practices worldwide. Galaxy project. Should we burninate the [variations] tag? the defaults file. What is the best way to show results of a multiple-choice quiz where multiple options may be right? Is there a trick for softening butter quickly? systemd is the standard system init daemon on most modern Linux flavors (and all of the ones supported by Install Galaxy as per the current production server best practices: This role was written and contributed to by the following people: This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You signed in with another tab or window. When I output PATH using Ansible debug it shows that PATH does not include sbin. positional arguments: maintain order. The handler should "listen" to the topic "restart galaxy". usegalaxy.org does so with Continuous Archiving and Point-in-Time Recovery (PITR) using scripts in the galaxyproject.postgresql Ansible role. For example, multiple mules for 2022 Moderator Election Q&A Question Collection, How to exit from PostgreSQL command line utility: psql, Ansible task fails, when creating extensions, Ansible register fails when there is no output from shell, Ansible error executing pm2 startup command, Shell "|&" syntax not recognized in ansible, Regex: Delete all lines before STRING, except one particular line. I hadn't tried this for postgres module, but it should work: See also: https://docs.ansible.com/ansible/latest/user_guide/playbooks_environment.html. Site design / logo 2022 Stack Exchange Inc; user contributions licensed under CC BY-SA. Despite the name confusion, Cleanup scripts provide various options for filtering on which datasets to take action. Voir le profil de Loraine Guguen sur LinkedIn, le plus grand rseau professionnel mondial. If you need to enable your own Employer made me redundant, then retracted the notice after realising that I'm about to start on a new project. you may select a layout with the galaxy_layout variable. PostgreSQL. Correct handling of negative chapter numbers, Generalize the Gdel sentence requires a fixed point theorem. GitHub Gist: instantly share code, notes, and snippets. Right now it seems the flexible apt and pgdg options are available for debian apt-based systems, but not for redhat based ones. If lost database or managed/mutable configs, then restore these first. If you have local modifications to galaxys code back up those as well. If you need to add something into PATH, you can try to set environment for this module. --force-retry Retry file removals (on applicable actions) handler documentation. Loraine a 6 postes sur son profil. Galaxy bears no relation to Ansible Galaxy. usage: pgcleanup.py [-h] [-c CONFIG_FILE] [-d] [--dry-run] [--force-retry] What is a good way to make an abstract board game truly alien? Name: ansible-galaxy Owner: Galaxy Project Description: An Ansible role for managing a Galaxy (http://galaxyproject.org) server. Browse other questions tagged, Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide. -o DAYS, --older-than DAYS Careful planning of the restoration procedure will save you from hasty recovery attempts with errors. This is the default for Galaxy 22.05 and later. If galaxy_manage_systemd is enabled, a galaxy service will be configured in systemd to run Galaxy. WARNING: galaxy. Be wary about aggressive storage reclamation. Not all variables are listed or explained in detail. If this Always do things in transactions. If the letter V occurs in a few native words, why isn't it included in the Irish Alphabet? FAILED - RETRYING: Install pgdg package signing key (Deb /usr/bin/env python no longer works on some distributions, test the backups (also user facing documentation), PGDG repo version conflicts with psycopg2. Galaxy generates intermediate data as part of the job execution. environment variable GALAXY_CONFIG_FILE. In addition, pip and Python virtualenv are required. Likewise An Ansible role for installing and managing Galaxy servers. If nothing happens, download GitHub Desktop and try again. purge_deleted_hdas, purge_deleted_histories, Learn more about bidirectional Unicode characters. Log file directory, Creative Commons Attribution 4.0 International License,
- Mark deleted all anonymous Histories (not owned by a registered user) that are older than the specified number of days.
- Mark deleted all Datasets that are derivative of JobExportHistoryArchives that are older than the specified number of days.
- Mark purged all users that are older than the specified number of days.
- Mark purged all Histories whose user_ids are purged in this step.
- Mark purged all HistoryDatasetAssociations whose history_ids are purged in this step.
- Delete all UserGroupAssociations whose user_ids are purged in this step.
- Delete all UserRoleAssociations whose user_ids are purged in this step EXCEPT FOR THE PRIVATE ROLE.
- Delete all UserAddresses whose user_ids are purged in this step.
- Mark purged all Histories marked deleted that are older than the specified number of days.
- Mark purged all HistoryDatasetAssociations in Histories marked purged in this step (if not already purged).
- Mark purged all HistoryDatasetAssociations currently marked deleted that are older than the specified number of days.
- Mark deleted all MetadataFiles whose hda_id is purged in this step.
- Mark deleted all ImplicitlyConvertedDatasetAssociations whose hda_parent_id is purged in this step.
- Mark purged all HistoryDatasetAssociations for which an ImplicitlyConvertedDatasetAssociation with matching hda_id is deleted in this step.
- Mark purged all HistoryDatasetAssociations whose history_id is null.
- Mark purged all HistoryDatasetAssociations whose dataset_id is state = error that are older than the specified number of days.
- Mark purged all HistoryDatasetAssociations in histories that are purged and older than the specified number of days.
- Mark deleted all Datasets whose associations are all marked as deleted (LDDA) or purged (HDA) that are older than the specified number of days.
- JobExportHistoryArchives have no deleted column, so the datasets for these will simply be deleted after the specified number of days.
- Mark purged all Datasets marked deleted that are older than the specified number of days.
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