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Keywords: Galaxy 

Galaxy Proteomics workshop Prague 2018

Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic

Scientific topics: Proteomics

Keywords: Galaxy, training, proteomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Galaxy Proteomics workshop Prague 2018 https://tess.elixir-europe.org/materials/galaxy-proteomics-workshop-prague-2018 Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic Andrea Argentini Frederik Coppens Pavel Dvorak Matthias Fahrner Melanie Foell Björn Grüning Martin Hubalek Hana Pergl Sustkova Marek Vrbacky Proteomics Galaxy, training, proteomics, eLearning, EeLP life scientists Researchers PhD Students
ELIXIR TtR course: Basic genomics using advanced analysis tools

Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia

Scientific topics: Genomics

Keywords: Galaxy, training, Genomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

ELIXIR TtR course: Basic genomics using advanced analysis tools https://tess.elixir-europe.org/materials/elixir-ttr-course-basic-genomics-using-advanced-analysis-tools Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia Christophe Antoniewski Olivier Inizan Genomics Galaxy, training, Genomics, eLearning, EeLP life scientists beginner bioinformaticians Postgraduate students
PhenoMeNal: accessing metabolomics workflows in Galaxy

A description of PhenoMeNal and when to use it, the creation of a cloud research environment and how to access Galaxy workflows via PhenoMeNal.

Scientific topics: Chemical biology, Metabolomics

Keywords: Galaxy

PhenoMeNal: accessing metabolomics workflows in Galaxy https://tess.elixir-europe.org/materials/phenomenal-accessing-metabolomics-workflows-in-galaxy A description of PhenoMeNal and when to use it, the creation of a cloud research environment and how to access Galaxy workflows via PhenoMeNal. Chemical biology Metabolomics Galaxy Beginners
Exercices on Galaxy: metagenomics

Find Rapidly OTU with Galaxy Solution

Keywords: Galaxy, Metagenomics

Exercices on Galaxy: metagenomics https://tess.elixir-europe.org/materials/exercices-on-galaxy-metagenomics Find Rapidly OTU with Galaxy Solution Galaxy, Metagenomics
ToolShed upload and tool-iuc PR

Questions What is a Tool Shed? How to install tools and workflows from a Tool Shed into a Galaxy instance? What are the Tool Shed repository types? How to publish with Planemo? Objectives Discover what is a Tool Shed Be able to install tools and workflows from a Tool Shed into a...

Keywords: Galaxy

ToolShed upload and tool-iuc PR https://tess.elixir-europe.org/materials/toolshed-upload-and-tool-iuc-pr Questions What is a Tool Shed? How to install tools and workflows from a Tool Shed into a Galaxy instance? What are the Tool Shed repository types? How to publish with Planemo? Objectives Discover what is a Tool Shed Be able to install tools and workflows from a Tool Shed into a Galaxy instance Be able to publish tools with Planemo Galaxy
BioBlend API

BioBlend module, a python library to use Galaxy API

Keywords: API, Galaxy, Python

BioBlend API https://tess.elixir-europe.org/materials/bioblend-api BioBlend module, a python library to use Galaxy API API, Galaxy, Python
Galaxy Visualisation - Slides

Questions How can visualization plugins benefit science? Objectives Implement a first Galaxy visualization Understand the client side vs. server side principle

Keywords: Galaxy

Galaxy Visualisation - Slides https://tess.elixir-europe.org/materials/galaxy-visualisation-slides Questions How can visualization plugins benefit science? Objectives Implement a first Galaxy visualization Understand the client side vs. server side principle Galaxy
Galaxy Configuration Hierarchy

How to configure your local instance of Galaxy

Keywords: Galaxy

Galaxy Configuration Hierarchy https://tess.elixir-europe.org/materials/galaxy-configuration-hierarchy How to configure your local instance of Galaxy Galaxy
Galaxy Interactive Tour

Questions What is a Galaxy Interactive Tour? How to create a Galaxy Interactive Tour? Objectives Discover what is a Galaxy Interactive Tour Be able to create a Galaxy Interactive Tour Be able to add a Galaxy Interactive Tour in a Galaxy instance

Keywords: Galaxy

Galaxy Interactive Tour https://tess.elixir-europe.org/materials/galaxy-interactive-tour Questions What is a Galaxy Interactive Tour? How to create a Galaxy Interactive Tour? Objectives Discover what is a Galaxy Interactive Tour Be able to create a Galaxy Interactive Tour Be able to add a Galaxy Interactive Tour in a Galaxy instance Galaxy
Tool development and integration into Galaxy

Questions: What is a tool for Galaxy? How to build a tool/wrapper with the good practices? How to deal with the tool environment? Objectives: Discover what is a wrapper and its structure Use the Planemo utilities to develop a good wrapper Deal with the dependencies Write functional...

Keywords: Galaxy

Tool development and integration into Galaxy https://tess.elixir-europe.org/materials/tool-development-and-integration-into-galaxy Questions: What is a tool for Galaxy? How to build a tool/wrapper with the good practices? How to deal with the tool environment? Objectives: Discover what is a wrapper and its structure Use the Planemo utilities to develop a good wrapper Deal with the dependencies Write functional tests Make a tool ready for publishing in a ToolShed Galaxy
Galaxy Installation

How to install a local instance of Galaxy

Keywords: Galaxy

Galaxy Installation https://tess.elixir-europe.org/materials/galaxy-installation How to install a local instance of Galaxy Galaxy
Galaxy Handlers

Galaxy is a web application that uses handlers to perform actions. There are two main types of actions that are carried out by handlers: Respond to user requests; These actions are carried out by web handlers Manage the execution of tools; These actions are performed by job handlers. By...

Keywords: Galaxy

Galaxy Handlers https://tess.elixir-europe.org/materials/galaxy-handlers Galaxy is a web application that uses handlers to perform actions. There are two main types of actions that are carried out by handlers: Respond to user requests; These actions are carried out by web handlers Manage the execution of tools; These actions are performed by job handlers. By default, Galaxy is configured to run a single handler that handles both user queries and jobs. Depending on the number of users accessing your Galaxy instance or the number of jobs you need to manage you may need to start web handlers or additional job handlers. Galaxy
Development in Galaxy

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Here, you will find some materials to learn how to contribute to Galaxy project.

Keywords: Galaxy

Development in Galaxy https://tess.elixir-europe.org/materials/development-in-galaxy Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Here, you will find some materials to learn how to contribute to Galaxy project. Galaxy
Training on Galaxy : Metagenomics

Find Rapidly OTU with Galaxy Solution

Keywords: Galaxy, Metagenomics

Training on Galaxy : Metagenomics https://tess.elixir-europe.org/materials/training-on-galaxy-metagenomics Find Rapidly OTU with Galaxy Solution Galaxy, Metagenomics
Initiation to Galaxy

DNA-sequence analysis: from raw reads to variants calling within the galaxy environement.

Keywords: DNA Analysis, Galaxy, Variant calling

Initiation to Galaxy https://tess.elixir-europe.org/materials/initiation-to-galaxy DNA-sequence analysis: from raw reads to variants calling within the galaxy environement. DNA Analysis, Galaxy, Variant calling
Docker and Galaxy

Questions Why Docker? What is it? How to use Docker? How to integrate Galaxy in Docker to facilitate its deployment? Objectives Docker basics Galaxy Docker image (usage) Galaxy Docker (internals) Galaxy flavours

Keywords: Docker, Galaxy

Docker and Galaxy https://tess.elixir-europe.org/materials/docker-and-galaxy Questions Why Docker? What is it? How to use Docker? How to integrate Galaxy in Docker to facilitate its deployment? Objectives Docker basics Galaxy Docker image (usage) Galaxy Docker (internals) Galaxy flavours Docker, Galaxy
Connecting Galaxy to a compute cluster

Problems Running jobs on the Galaxy server negatively impacts Galaxy UI performance Even adding one other host helps Can restart Galaxy without interrupting jobs Solution: Connecter Galaxy to a computing cluster

Keywords: Cluster, Galaxy

Connecting Galaxy to a compute cluster https://tess.elixir-europe.org/materials/connecting-galaxy-to-a-compute-cluster Problems Running jobs on the Galaxy server negatively impacts Galaxy UI performance Even adding one other host helps Can restart Galaxy without interrupting jobs Solution: Connecter Galaxy to a computing cluster Cluster, Galaxy
Galactic Database

How to choose a database for Galaxy and configure it

Keywords: Galaxy

Galactic Database https://tess.elixir-europe.org/materials/galactic-database How to choose a database for Galaxy and configure it Galaxy
Users, Groups, and Quotas in Galaxy

How to handle Users, Groups, and Quotas in Galaxy

Keywords: Galaxy

Users, Groups, and Quotas in Galaxy https://tess.elixir-europe.org/materials/users-groups-and-quotas-in-galaxy How to handle Users, Groups, and Quotas in Galaxy Galaxy
Defining and importing genomes, Data Managers into Galaxy

Intro to built in datasets Built in data hierarchy Some problems Data Managers

Keywords: Galaxy

Defining and importing genomes, Data Managers into Galaxy https://tess.elixir-europe.org/materials/defining-and-importing-genomes-data-managers-into-galaxy Intro to built in datasets Built in data hierarchy Some problems Data Managers Galaxy
Galaxy Docker Training Tutorial

Galaxy docker integration Enable Galaxy to use BioContainers (Docker) Galaxy with Docker swarm

Keywords: Docker, Galaxy

Galaxy Docker Training Tutorial https://tess.elixir-europe.org/materials/galaxy-docker-training-tutorial Galaxy docker integration Enable Galaxy to use BioContainers (Docker) Galaxy with Docker swarm Docker, Galaxy
Galaxy Administration

How to use the administation panel of Galaxy

Keywords: Galaxy

Galaxy Administration https://tess.elixir-europe.org/materials/galaxy-administration How to use the administation panel of Galaxy Galaxy
(Proxy) Web Server Choices and Configuration

Installation and configuration of NGiNX for Galaxy

Keywords: Galaxy, NGiNX

(Proxy) Web Server Choices and Configuration https://tess.elixir-europe.org/materials/proxy-web-server-choices-and-configuration Installation and configuration of NGiNX for Galaxy Galaxy, NGiNX
Mapping reads on Galaxy server

This is the presentation of the first Galaxy workshop

Keywords: Galaxy, IBERS, Institute of Biological, Environmental and Rural Sciences

Mapping reads on Galaxy server https://tess.elixir-europe.org/materials/mapping-reads-on-galaxy-server This is the presentation of the first Galaxy workshop Galaxy, IBERS, Institute of Biological, Environmental and Rural Sciences