To get you started, check our dedicated tutorials or our Frequently Asked Questions Basics Session: November 7-8. The three day advanced session will build on topics covered in the basics section. The first ever Galaxy Project Admin Training workshop will be held November 7-11 in Salt Lake City, Utah. ), Optionally sets a password to the machine. 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. Skip to the section on setting up below that is appropriate for you. 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. Did you use this material as an instructor? Most of the workshop will happen at the Linux command line. . 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. Place this in the GAT Machines spreadsheet in the correct tab. Shah Alam, Selangor, Malaysia. I have completed the cloud computing certification alongwith salesforce admin adm201 training.. Trainer was my mentor and had guided with his best teaching experience..He . The basics section will end on Tuesday evening with an overview of Galaxy's architecture. Welcome & Setup (Start Here!) Database choices and configuration. Infrastructure is available for running GATs for free from UseGalaxy.eu, This can be very convenient and easy to use. This is an asynchronous event. Contact [Galaxy Outreach](mailto:outreach@galaxyproject.org), Comfortable with the Unix/Linux command line, Some experience with Linux Package Management. Instructors are from the Galaxy Project Team and the Galaxy Community: Participants can register for one or both workshops. 5 days, 106 registrations, 29 countries, 12.5 hours of video and 100% awesomeness. You can specify ansible_user=something if it uses a different username, and ansible_password=password for each machine. 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. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Project Team. Logistics Introduction to Galaxy . However, this distinction of regions is not necessary. Logistics ), (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. admin-training has no bugs, it has no vulnerabilities and it has low support. Publicity. Registration 1. The three day advanced session will build on topics covered in the basics section. 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. If you have your own cloud, setup VMs per student. 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. These can be in any part of Galaxy, not just the core engine, and includes training, documentation, and other software. 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. All prerequisites from the Basic Topics workshop. usegalaxy.org.au is supported by Bioplatforms Australia and the Australian Research Data Commons. EU provides appropriate DNS entries so you can run trainings with ITs. ns2.gname.net @ represents the DNS zone origin galaxytraining.net as often found in BIND zone files. 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! usegalaxy.org.au is supported by Bioplatforms Australia and the Australian Research Data Commons. Basic and Advanced Topics sessions will be offered and participants can register for one or both. To give a user admin privileges add the user's Galaxy login email to the configuration file config/galaxy.yml. Database choices and configuration (SQLite & PostgreSQL), Web server choices and configuration (NGINX & Apache), Identifying and installing well-defined tools from the Galaxy Tool Shed. This workshop will cover what you need to know to set up your own production, high . 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. A Very Short Introduction to Galaxy Lecture & Demo Video Participants will learn how to . To control Galaxy through the UI (installing tools, managing users, creating groups, etc. Now youll need to bootstrap the instances and prepare them for student use. Whatever is your background, there is probably a way to do it: via the GitHub website, via command-line. Youll need to be competent in at least one of them before the workshop starts. 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. Questions? Ansible Essential Training Administrative Human Resources Lihat semua kursus Lencana profil awam Haifa Nadia Sertakan profil LinkedIn ini di laman web lain . Participants will learn how to install, configure, customize, and extend their own Galaxy servers. If you don't have the file set it up using the instructions above. Module: Galaxy Admin Training . admin.gname.net. Module: Galaxy Admin Training . Registration is available on first come, first served basis. The Galaxy Admins and the GTN instructors community has just run the largest-ever Galaxy Admin training event. This is a hub page on topics related to deployment and administration of your own instance of Galaxy. Advanced Session| Once deployed, clone/pull the repository locally and run ./bin/process-training-output.sh. Learn how to run a Galaxy server. This is one of three comprehensive Galaxy admin and developer training events between November and February. This tutorial has multiple audiences who are all adressed within this one tutorial. Use this timeline to help keep track of where you are in GalaxyAdmin Training. Basics Session 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. This two day basics session will introduce participants to what you need to know to get a Galaxy server up . Additionally images and complex formatting is easy. If you don't have a GitHub or Gitter account yet, then set them up (in that order). 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. Does http://localhost:8080/api/version respond with, Does https://localhost:443/api/version respond with. In the hosts file, edit the [workshop_eu] section to list all of your IPs or DNS entries. Galaxy Server administration. Most of the training should be fine, but sometimes changes in e.g. 140 pengikut 140 kenalan. *, 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. 2. Topic order and specific start and end times are likely to change. All participants in the advanced session are also welcome to attend this session at the Salt Lake City Library. Galaxy Training! Ten Simple Rules for Setting up a Galaxy Instance as a Service. 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. Remove the workshop_oz from the top of the file under [workshop_instances:children]. Place the list of usernames and IPs and passwords in the GAT Machines spreadsheet in the correct tab. Can't make it to Salt Lake or on another continent? After the Training. Full Story We will use compute resources from the University of Utah Center for High Performance Computing (CHPC) for cluster access during the advanced session. GalaxyAdmin Training Path The yearly GalaxyAdmin Training follows a specific ordering of tutorials. 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. 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. Administrative Executive at Galaxy Aerospace (M) Sdn. See the Registration page for dates, rates, and other details. Do you have your own infrastructure, or do you need to request infrastructure? The roles that are used in these training are currently used by use galaxy. It is being held in Salt Lake City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16) meets in Salt Lake. 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 . This is useful when your machines only have an SSH key on them, and no password set for students. . Introduction to the Galaxy Tool Shed: Identifying and installing well-defined tools. 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 Feel free to give us feedback on how it went. 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. Practical information about this course and getting everything set up to follow this course. ), user must become an administrator. Make sure you rename it correctly. 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. So we developed a small utility, the gat-cli, which assists in monitoring students progress. This is seen in the workshop_eu and workshop_oz groups, and the corresponding commands in the Makefile. 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). Setup a python virtualenv and activate it. All participants should bring a wifi-enabled laptop with. We are working with the Utah High Performance Computing Center at the University of Utah for cluster access during the advanced session. 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 Step 13 reports Step 14 ftp 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. This session both extends those topics, such as tool definition, and adds new ones, such as working with compute clusters and heterogeneous resources. Here is an example pull request when we did this after BCC2020. We recommend providing a website similar to our GitHub repository (or using our repository! To give a Galaxy user admin privileges you have to add their Galaxy login ( email ) to the Galaxy configuration file config/galaxy.yml. Training will take place the week before Supercomputing'16 (SC16) meets in Salt Lake. Get to know it. Please review the prerequisites carefully before registering. 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. Contact [Galaxy Outreach](mailto:outreach@galaxyproject.org). Once your VMs are running, great! 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. (others coming soon.) Get a basic Galaxy server up and running. The last command runs the playbook.yml, which in turn does a large number of things: Once your VMs are ready, you should test ALL of the lessons you intend to teach. This tutorial has multiple audiences who are all adressed within this one tutorial. If you arent comfortable with this before you arrive, then you will be lost the entire time. 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. There are other make check- commands for each of the gat status commands. ; Data Managers, Extending your installation: Enabling FTP & SMTP. Basic and Advanced Topics sessions will be offered and participants can register for one or both. Galaxy Admin hosts successful EOSC-Life-funded online training The January 2021 course included 59 participants from 5 continents. 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. 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. How comfortable do you need to be? 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 . If you arrive without meeting the prerequisites then the workshop will be a frustrating experience. There you can learn to integrate webhooks . 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. You need to have a solid grasp of the, Linux command line, a text editor, and Linux package management. This two day introductory session will cover how to: See the Basics Session page for details and prerequisites. Basics Session We developed our structured 10-week Galaxy Certification Course to address both of your challenges. This is a short walk from the University Guest House, where participants are staying. Topics covered include. A recent version of either the Chrome or Firefox web browser installed. Course Logistics The Format. For information on event lodging, arriving in Salt Lake, and getting around, see the Event Logistics page. 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. Start here if you are new to Galaxy. Galaxy versions or the availability of newer versions of some ansible modules will indicate you should test the training as you plan to teach it, and update the training materials where relevant. Bhd. Galaxy Architecture Session, Tuesday evening, November 7. Sessions will be intensive and hands-on, and taught by experienced instructors from the Galaxy Project Team. If you arrive without meeting the prerequisites then the workshop will be a frustrating experience. Advanced Session| IEVISION is one of the first Salesforce ADM 201 training provider in Berlin city in GERMANY. 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. Read the full report for all the numbers, details, conclusions and feedback. If you are running Linux or Mac OS, then you already have this. 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. Related Keywords. Use this timeline to help keep track of where you are in Galaxy Admin Training. 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. Software to access the command line of a Linux server. Install the requirements (listed in requirements.txt). Understanding of material covered in the Basic Topics workshop. Sertai untuk berhubung . Learn how to run a Galaxy server. The advanced session will be held at the Commanders House on the University of Utah campus. 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. The workshop offers a 2 day introductory session followed by a 3 day advanced topics session.Participants can register for one or both sessions. * Could include. If the file does not exist yet you can create it from the provided sample (config/galaxy.yml.sample). Data Driven Research for Everyone Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research. 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. Each of these commands run a couple checks on their local machine. Deploying a compute cluster in OpenStack via Terraform: Will the training be online or in person? Topics include tool configuration, authentication and user management, using heterogeneous storage and compute services, and many other topics that will enable you to get your own Galaxy server up and running, performing well, and used by your community. 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. We'll be meeting in Conference Room 4 . Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface. usegalaxy.org.au is supported by Bioplatforms Australia and the Australian Research Data Commons. See the Advanced Session page for details and prerequisites. They are included here to give you an idea of the depth of knowledge that is required. Topic order and specific start and end times are likely to change. 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. Heres a sampling of commands and concepts that you should be comfortable with: Note: This is not an exhaustive list (or even a proper subset) of the commands that will be used in the workshop. 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. Galaxy Installation with Ansible: slides slides - tutorial hands-on; Time estimation: 30 minutes. Linux has several text editors available in it. Galaxy Admin Training 2016 is a weeklong event offering basic and advanced sessions. 1616133237 7200 3600 1209600 1800: @ A: 154.204.248.3 @ NS: . Registration admin-training is a Shell library typically used in Devops, Continuous Deployment, Ansible, Nginx, Docker applications. E.g. Only registered users can become admins. 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). Note that you have to restart Galaxy after modifying the configuration for changes to take effect. Please review the prerequisites carefully before registering. The most simple hosts file looks like: git clone https://github.com/galaxyproject/admin-training/ and change into that repo. This is a short walk from the University Guest House, where participants are staying. ), (When pulsar is in use) the pulsar machines are provisioned identically to the ones where, Installs basic dependencies (emacs, vim, nano, git, etc. This two day workshop will cover the big picture, and installation, configuration, and customization basics. The domain has been registered . World Class Training, Live Salesforce Project, 100% Placement* at lowest cost. We use a more complicated hosts file in the project, as we have multiple pools of VMs across global regions. We would like to thank the USTAR Center for Genetic Discovery (UCGD) for a grant to book this great venue for the advanced workshop. If you feel it is too much, you can even write it with any text editor and contact us: we will work together to integrate it. The first ever Galaxy Project Admin Training workshop will be held November 7-11 in Salt Lake City, Utah. 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. Admin UI, Log files, Direct database queries, Command line & scripts, What to backup and how, Advanced tool definition: visualizations, data managers, Questions? galaxy training: Galaxytraining Frequently Asked Questions (FAQ) Who is Galaxytraining.net? 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