Registration For information on event lodging, arriving in Salt Lake, and getting around, see the Event Logistics page. Instructors are from the Galaxy Project Team and the Galaxy Community: Participants can register for one or both workshops. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Project Team. Introduction to. . Course Duration: 5 Days Daily Schedule: 11 AM - 6 PM EST / 8 AM - 3 PM PST / 10 AM - 6 PM CET Where: Dalet iLearn - Interactive Online Learning Environment Fees: 1,800 / $1,800 Seats: Limited to 10 Training will take place the week before Supercomputing'16 (SC16) meets in Salt Lake. The three day advanced session will build on topics covered in the basics section. Most of the training should be fine, but sometimes changes in e.g. Participants will learn how to install, configure, customize, and extend their own Galaxy servers. (others coming soon.) Contact [Galaxy Outreach](mailto:outreach@galaxyproject.org), * *We are exploring combining the final dinner and the open questions sessions into a single informal and pizza-fueled open discussion session. First consider the requirements for your training: We recommend checking out an example schedule from the GAT repository and modifying it based on your needs. Registration The 2019 Galaxy Admin Training will be offered January 28 through February 1 at Penn State University (where the Galaxy Project got started over ten years ago). Comment: Galaxy Step 1 ansible-galaxy Step 2 tus Step 3 cvmfs Step 4 singularity Step 5 tool-management Step 6 data-library Step 7 connect-to-compute-cluster Step 8 job-destinations Step 9 pulsar Step 10 gxadmin Step 11 monitoring Step 12 tiaas reports ftp Installing Singularity First, we will install Singularity using Ansible. 1. setup VMs which are accessible from where your students are, expose ports 20, 80, 443 (optional), 8080 (optional but nice), Bootstraps python on the machine if it isnt available already (Ubuntu stopped including it for some reason. Sertai untuk berhubung . A Very Short Introduction to Galaxy Lecture & Demo Video Basics Session: November 7-8. During the course, your System Admin will: Learn best practices for base configuration in the core modules and the eGalaxy Web Store. So we developed a small utility, the gat-cli, which assists in monitoring students progress. This tutorial has multiple audiences who are all adressed within this one tutorial. Software to access the command line of a Linux server. Galaxy Admin hosts successful EOSC-Life-funded online training The January 2021 course included 59 participants from 5 continents. Tutorial Content is licensed under Creative Commons Attribution 4.0 International License, checking out an example schedule from the GAT repository, FAQ page for the Teaching and Hosting Galaxy training topic, https://training.galaxyproject.org/archive/2021-11-01/topics/instructors/tutorials/galaxy-admin-training/tutorial.html. usegalaxy.org.au is supported by Bioplatforms Australia and the Australian Research Data Commons. You can specify ansible_user=something if it uses a different username, and ansible_password=password for each machine. Well be using Ubuntu based images during the workshop, which means well be using apt to do package management. Module: Galaxy Admin Training . Questions? If the file does not exist yet you can create it from the provided sample (config/galaxy.yml.sample). Basic and Advanced Topics sessions will be offered and participants can register for one or both. Administrative Executive at Galaxy Aerospace (M) Sdn. The GAT team maintains some infrastructure to handle the bootstrapping in the GAT repository. usegalaxy.org.au is supported by Bioplatforms Australia and the Australian Research Data Commons. The most simple hosts file looks like: git clone https://github.com/galaxyproject/admin-training/ and change into that repo. There are other make check- commands for each of the gat status commands. Having actual experience with setting up and running your own Galaxy server. Use this timeline to help keep track of where you are in GalaxyAdmin Training. 140 pengikut 140 kenalan. All participants in the advanced session are also welcome to attend this session at the Salt Lake City Library. galaxy training: Galaxytraining Frequently Asked Questions (FAQ) Who is Galaxytraining.net? Contact [Galaxy Outreach](mailto:outreach@galaxyproject.org). Start here if you are new to Galaxy. usegalaxy.org is supported by NIH and NSF Grants HG006620, 1661497, and 1929694. usegalaxy.eu is supported by the German Federal Ministry of Education and Research grant 031L0101C and de.NBI-epi. *, and other, servers in maintaining their infrastructure. Install the requirements (listed in requirements.txt). Bhd. When an admin user logs into Galaxy, they will see an "Admin" menu item in the top Galaxy menu bar which will take them to the Galaxy Admin page with an administration panel. I'm wondering about the contents of this nd how it relates to the Galaxy Administrator Training being done (. GalaxyAdmin Training Path The yearly GalaxyAdmin Training follows a specific ordering of tutorials. Get a copy of the workshop server up and running. Get a basic Galaxy server up and running. usegalaxy.org is supported by NIH and NSF Grants HG006620, 1661497, and 1929694. usegalaxy.eu is supported by the German Federal Ministry of Education and Research grant 031L0101C and de.NBI-epi. There you can learn to integrate webhooks . Teaching online is slower, so you may not be able to cover as many topic as in person; you may also need more helpers. If you are running Windows than youll need to get something like putty installed before the workshop. If you don't have a GitHub or Gitter account yet, then set them up (in that order). Run make to list all of them. After the Training. Participants will finish this workshop with a solid understanding of how to set up and customize a Galaxy instance running on a desktop or standalone server. Please review the prerequisites carefully before registering. When an admin user logs into Galaxy, they will see an "Admin" menu item in the top Galaxy menu bar which will take them to the Galaxy Admin page with an administration panel. It is deployed at large and small organizations around the world and used in a broad range of biomedical research domains, and across the tree of life. Introduction to Galaxy . These can be in any part of Galaxy, not just the core engine, and includes training, documentation, and other software. This two day introductory session will cover how to: See the Basics Session page for details and prerequisites. admin-training is a Shell library typically used in Devops, Continuous Deployment, Ansible, Nginx, Docker applications. This two day introductory session will introduce participants to what you need to know to get a Galaxy server up and running on a standalone server. It is being held in Salt Lake City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16) meets in Salt Lake. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Project Team. We are working with the Utah High Performance Computing Center at the University of Utah for cluster access during the advanced session. 06-03-2020 13:30 Galaxy Admin Training week will be offered 2-6 March 2020 at the Barcelona Supercomputing Center (BSC) in Barcelona, Spain. If you arrive without meeting the prerequisites then the workshop will be a frustrating experience. The slides and tutorials for your training. Data Driven Research for Everyone Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research. Publicity. The workshop offers a 2 day introductory session followed by a 3 day advanced topics session.Participants can register for one or both sessions. Introduction to, Web server choices and configuration. University of Utah Center for High Performance Computing (CHPC), USTAR Center for Genetic Discovery (UCGD), Clinical & Translational Science Biomedical Informatics Core (CCTS BMIC), Database choices and configuration (SQLite & PostgreSQL), Web server choices and configuration (NGINX & Apache), Identifying and installing well-defined tools from the Galaxy Tool Shed, Interactive environments: development and deployment, Using and configuring external authentication services, Using public and private cloud compute resources, Storage management and using heterogeneous storage services, Customizing and extending your Galaxy code. Ten Simple Rules for Setting up a Galaxy Instance as a Service. Can't make it to Salt Lake or on another continent? To give a Galaxy user admin privileges you have to add their Galaxy login ( email ) to the Galaxy configuration file config/galaxy.yml. All prerequisites from the Basic Topics workshop. Learn how to run a Galaxy server. If you are new to Galaxy and want to administer your own service read the Ten Simple Rules for Setting up a Galaxy Instance as a Service. ns2.gname.net @ represents the DNS zone origin galaxytraining.net as often found in BIND zone files. If you do not have a cloud available that can, at minimum: Then consider contacting UseGalaxy.eu and let us know youd like to host a GAT event. Make sure you rename it correctly. This two day basics session will introduce participants to what you need to know to get a Galaxy server up . If you are a Galaxy user or admin, you can create, or tag existing GitHub issues for any irritating, but likely easily fixed bugs (make a guess). Understanding of material covered in the Basic Topics workshop. This is an incredibly exciting development for our first official Gallantries event, but it's also a bit terrifying as none of us have run such a big event before. If you are running Linux or Mac OS, then you already have this. Lodging, the airport, and all training events are on the University of Utah campus or in downtown Salt Lake City, and all are easily accessible using TRAX, Salt Lake's light rail network. To give a user admin privileges add the user's Galaxy login email to the configuration file config/galaxy.yml. Registration is available on first come, first served basis. Galaxy Server administration language . We will use compute resources from the University of Utah Center for High Performance Computing (CHPC) for cluster access during the advanced session. We encourage everyone involved in hosting a GAT event to read this, so you are aware of all of the moving parts which are required for such an event. Shah Alam, Selangor, Malaysia. This is a short walk from the University Guest House, where participants are staying. The basics section will end on Tuesday evening with an overview of Galaxy's architecture. You'll also learn and how to extend your Galaxy with your own tools and tools from the community, and how to define reference data in your server as well. *, University of Utah Center for High Performance Computing (CHPC), material covered in the Basic Topics workshop, USTAR Center for Genetic Discovery (UCGD), Updating tools and supporting multiple versions of tools, Using and configuring external authentication services, Using public and private cloud compute resources, Advanced Tool Definitions: Error Handling, Storage management and using heterogeneous storage services, Advanced tool definition: data types and data sources, Participant selected topics and open questions. They are: We would like to thank the University of Utah Center for High Performance Computing (CHPC) for compute infrastructure support, and the USTAR Center for Genetic Discovery (UCGD), Department of Biomedical Informatics and the Clinical & Translational Science Biomedical Informatics Core (CCTS BMIC) at the University of Utah for hosting this event. If you don't have the file set it up using the instructions above. This is seen in the workshop_eu and workshop_oz groups, and the corresponding commands in the Makefile. Galaxy Server administration. Deploying Install own Galaxy Run on the Cloud Infrastructure Maintaining an Instance Configuration Authentication and Authorization Production Configuration Installing Tools Logistics Once your training is concluded, go through the questions students have asked in the Google Doc, and consider contributing them back to the training materials with Tips and Question boxes covering these student questions. with at minimum the following links: During planning for BCC2020 we found that monitoring student progress would be extremely difficult, it was not a situation we had encountered before as this was the first remote GAT during the pandemic. Supporting Materials: Topic Overview slides . Get to know it. Only registered users can become admins. These Ansible roles and training materials were last tested on Centos 7 and Ubuntu 18.04, but will probably work on other RHEL and Debian variants. This workshop will cover what you need to know to set up your own production, high . Module: Galaxy Admin Training . The roles that are used in these training are currently used by use galaxy. Use this timeline to help keep track of where you are in Galaxy Admin Training. usegalaxy.org is supported by NIH and NSF Grants HG006620, 1661497, and 1929694. usegalaxy.eu is supported by the German Federal Ministry of Education and Research grant 031L0101C and de.NBI-epi. Whatever is your background, there is probably a way to do it: via the GitHub website, via command-line. This is a draft schedule and is a work in progress. We use a more complicated hosts file in the project, as we have multiple pools of VMs across global regions. Setting up and running a Galaxy Admin Training is not a very complicated process thanks to a significant amount of work that has been put into making it easy and quick. This repo includes an admin-corner for training material about administering Galaxy. ), (Generates if needed) and copies an SSH key to all of the machines to make login easier (this is stored in, This key is set as the ubuntu users key, and added to their authorized_keys, to permit them to run ansible easily on that machine (if they dont configure the local connection correctly. Defining and importing genomes, cont. Galaxy Installation with Ansible: slides slides - tutorial hands-on; Time estimation: 30 minutes. kubectl exec -it galaxy-web-7568c58b94-jzkvm /bin/bash Now run ls / galaxy /server/config/ and note that the galaxy .yml contains the content that you've provided and that custom_tool_conf.xml has also been mapped into the config folder. Starting on Wednesday the advanced session will be held at the Commanders House on the University of Utah campus. Rates depend on your organization's non-profit status and when you register. ), user must become an administrator. Topic order and specific start and end times are likely to change. These videos will introduce you to the Galaxy platform, and walk you through your first analyses. 2. Organizers will make sure that these editors are available on the Linux images we use in the workshop: You dont need to be an expert at Linux package management, but you do need to have some experience at installing and upgrading packages on a Linux system. We recommend providing a website similar to our GitHub repository (or using our repository! admin.gname.net. The -eu again refers to the specific pool of machines, and if youre using a different hosts file, with different group names, you may need to edit the Makefile accordingly. Galaxy Admin Training November 7-11, 2016 University of Utah Salt Lake City, Utah United States Register by October 16 Lodging released October 6 Basics Session Advanced Session| Registration Logistics Publicity November 7-8, Salt Lake City Library We developed our structured 10-week Galaxy Certification Course to address both of your challenges. Topic order and specific start and end times are likely to change. Publicity. Third time's a charm Join us for the third and final part of our Advanced Dalet Galaxy Admin Training course where we show you how to manage a site upgrade, metadata and media tools as well as . The three day advanced session will build on topics covered in the basics section. Learn how to run a Galaxy server. Youll need to be competent in at least one of them before the workshop starts. The introductory training workshop will be held at the Salt Lake City Main Public Library. On 25-29 January, 2021, the Galaxy Admin community hosted a workshop which covered introductory and advanced topics you need to know to set up your own production, high-performance and multi-user Galaxy instance. Does http://localhost:8080/api/version respond with, Does https://localhost:443/api/version respond with. If you have your own cloud, setup VMs per student. Skip to the section on setting up below that is appropriate for you. Everything you were taught in the past few days can be found in the Galaxy Admin Training repository, which mostly points to the admin section of the Galaxy Training Materials.. For those of you who also need to do some Galaxy development, there is a dev section of training materials for those topics as well. Questions? Place this in the GAT Machines spreadsheet in the correct tab. Additionally images and complex formatting is easy. However, this distinction of regions is not necessary. We'll be meeting in Conference Room 4 . E.g. ), (When pulsar is in use) the pulsar machines are provisioned identically to the ones where, Installs basic dependencies (emacs, vim, nano, git, etc. See the Advanced Session page for details and prerequisites. Database choices and configuration (SQLite & PostgreSQL), Web server choices and configuration (NGINX & Apache), Identifying and installing well-defined tools from the Galaxy Tool Shed. Admin UI, Log files, Direct database queries, Command line & scripts, What to backup and how, Advanced tool definition: visualizations, data managers, Questions? If you arent comfortable with this before you arrive, then you will be lost the entire time. Contact [Galaxy Outreach](mailto:outreach@galaxyproject.org), Comfortable with the Unix/Linux command line, Some experience with Linux Package Management. In our experience this is an excellent format for discussion: it allows students to ask as many questions as they have, and responses can be given in real-time right below each question. usegalaxy.org is supported by NIH and NSF Grants HG006620, 1661497, and 1929694. usegalaxy.eu is supported by the German Federal Ministry of Education and Research grant 031L0101C and de.NBI-epi. ; Data Managers, Extending your installation: Enabling FTP & SMTP. Also make sure you don't specify it twice - the line with admin_users is already present in every sample config and should be there only once. How do I organise a Galaxy Admin Training (GAT), Interact with the UseGalaxy.eu admins to arrange for infrastructure. Galaxy Architecture Session, Tuesday evening, November 7. Step 1ansible-galaxy Step 2tus Step 3cvmfs Step 4singularity Step 5tool-management Step 6data-library Step 7connect-to-compute-cluster Step 8job-destinations Step 9pulsar Once deployed, clone/pull the repository locally and run ./bin/process-training-output.sh. Logistics World Class Training, Live Salesforce Project, 100% Placement* at lowest cost. The first ever Galaxy Project Admin Training workshop will be held November 7-11 in Salt Lake City, Utah. Once your VMs are running, great! Read the full report for all the numbers, details, conclusions and feedback. Deploying a compute cluster in OpenStack via Terraform: Will the training be online or in person? Use this timeline to help keep track of where you are in Galaxy Admin Training. Feel free to give us feedback on how it went. Each of these commands run a couple checks on their local machine. * Could include. This is a short walk from the University Guest House, where participants are staying. This two day workshop will cover the big picture, and installation, configuration, and customization basics. Friday Galaxy Admin Training November 7-11, 2016 University of Utah Salt Lake City, Utah United States Register by October 16 Lodging released October 6 Basics Session Advanced Session| Registration Logistics Publicity November 8-11, University of Utah Campus The three day advanced session will build on topics covered in the basics section. As such the Gallantries participated in the organisation of the 2021 Online Galaxy Admin Training, where we deployed the same methodology we intended to use during the Smrgsbord! This workshop will cover introductory and advanced topics you need to know to set up your own production, high-performance and multi-user Galaxy instance. Course Logistics The Format. Do you have your own infrastructure, or do you need to request infrastructure? ns1.gname.net. This is one of three comprehensive Galaxy admin and developer training events between November and February. Did you use this material as an instructor? This is useful when your machines only have an SSH key on them, and no password set for students. admin-training has no bugs, it has no vulnerabilities and it has low support. Introduction to the Galaxy Tool Shed: Identifying and installing well-defined tools. They are included here to give you an idea of the depth of knowledge that is required. All participants should bring a wifi-enabled laptop with. This is an asynchronous event. In case we get more registrations than we have spots available, the training team will connect with you to arrange another session. Ansible Essential Training Administrative Human Resources Lihat semua kursus Lencana profil awam Haifa Nadia Sertakan profil LinkedIn ini di laman web lain . For example the status-galaxy command checks: However, the gat command is only available on the VMs, so weve written an ansible task (wrapped in the Makefile) which SSHs into every machine, and runs the gat command for you: You can see a checkmark reported for every step completed by students, giving you a nice overview of how many students have completed each step, and if youre ready to move on. Ansible: . usegalaxy.org.au is supported by Bioplatforms Australia and the Australian Research Data Commons.
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