diff --git a/_layouts/topic.html b/_layouts/topic.html index 11cb16dd..bcde6963 100644 --- a/_layouts/topic.html +++ b/_layouts/topic.html @@ -44,53 +44,55 @@ {% for material in topic.material %} - - {{ material.title }} - - {% if material.type == "introduction" %} - - - {% if material.slides == "yes" %} - :mortar_board: - {% endif %} - - {% if topic.type != "admin-dev" %} - - - {% endif %} + {% if material.enable != "false" %} + + {{ material.title }} - {% elsif material.type == "tutorial" %} - - {% if material.hands_on == "external" %} - :link: - {% elsif material.hands_on == "yes" %} - :book: - {% elsif material.hands_on == "github" %} - :book: - {% endif %} - - - - {% if material.slides == "yes" %} - :mortar_board: + {% if material.type == "introduction" %} + + + {% if material.slides == "yes" %} + :mortar_board: + {% endif %} + + {% if topic.type != "admin-dev" %} + + {% endif %} - - {% if topic.type != "admin-dev" %} + {% elsif material.type == "tutorial" %} - {% if material.zenodo_link != "" %} - :open_file_folder: + {% if material.hands_on == "external" %} + :link: + {% elsif material.hands_on == "yes" %} + :book: + {% elsif material.hands_on == "github" %} + :book: {% endif %} - {% if material.galaxy_tour != "" %} - :eyes: + {% if material.slides == "yes" %} + :mortar_board: {% endif %} + + {% if topic.type != "admin-dev" %} + + {% if material.zenodo_link != "" %} + :open_file_folder: + {% endif %} + + + + {% if material.galaxy_tour != "" %} + :eyes: + {% endif %} + + {% endif %} {% endif %} - {% endif %} - + + {% endif %} {% endfor %} diff --git a/topics/admin/metadata.yaml b/topics/admin/metadata.yaml index 2072d8cd..d38c03d7 100644 --- a/topics/admin/metadata.yaml +++ b/topics/admin/metadata.yaml @@ -17,24 +17,19 @@ material: galaxy_tour: "" hands_on: "github" slides: "no" - questions: - "" - "" - objectives: - "" - "" - "" - time_estimation: "1d/3h/6h" - key_points: - "" - "" - "" - "..." - - title: "Galaxy Database schema" type: "tutorial" @@ -43,23 +38,18 @@ material: galaxy_tour: "" hands_on: "yes" slides: "no" - questions: - "Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that" - "How to extract usage information, which can not be gathered using the given report tools" - "How to move from MySQL to PostgreSQL" - "Is there ever a need to manually change the contents of a table" - objectives: - "Learn some of the design concepts of the Galaxy database" - "Extract information from the Galaxy database" - "Get to know SchemaSpy" - time_estimation: "2h" - key_points: - "Be careful, when you interact with the Galaxy database. And make sure you always have a backup!" - - title: "Docker and Galaxy" type: "tutorial" @@ -68,20 +58,16 @@ material: galaxy_tour: "" hands_on: "no" slides: "yes" - 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" - time_estimation: "1d/3h/6h" - key_points: - "Use Docker" - "Integrate your tools into Galaxy" @@ -92,6 +78,7 @@ material: name: "advanced-galaxy-customisation" slides: "yes" + maintainers: - name: "Björn Grüning" diff --git a/topics/assembly/metadata.yaml b/topics/assembly/metadata.yaml index cbe8ceba..51de124c 100644 --- a/topics/assembly/metadata.yaml +++ b/topics/assembly/metadata.yaml @@ -27,7 +27,6 @@ material: name: "general-introduction" zenodo_link: "https://doi.org/10.5281/zenodo.582600" galaxy_tour: "" - hands_on: "yes" slides: "yes" questions: - "How do we perform a very basic genome assembly from short read data?" @@ -39,8 +38,6 @@ material: - "We assembled some Illumina fastq reads into contigs using a short read assembler called Velvet" - "We showed what effect one of the key assembly parameters, the k-mer size, has on the assembly" - "It looks as though there are some exploitable patterns in the metric data vs the k-mer size." - - - title: "De Bruijn Graph Assembly" type: "tutorial" diff --git a/topics/chip-seq/metadata.yaml b/topics/chip-seq/metadata.yaml index ec23168e..91639426 100644 --- a/topics/chip-seq/metadata.yaml +++ b/topics/chip-seq/metadata.yaml @@ -33,12 +33,10 @@ material: hands_on: "yes" slides: "no" edam_ontology: "topic_3169" - questions: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of Tal1? - Which genes are regulated by Tal1? - objectives: - Inspect read quality with FastQC - Perform read trimming with Trimmomatic @@ -48,15 +46,12 @@ material: - Determine unique/common Tal1 binding sites from G1E and Megakaryocytes - Identify unique/common Tal1 peaks occupying gene promoters - Visually inspect Tal1 peaks with Trackster - requirements: - title: "Trackster" type: "external" link: "https://wiki.galaxyproject.org/Learn/Visualization" - time_estimation: "3h" - key_points: - Sophisticated analysis of ChIP-seq data is possible using tools hosted by Galaxy - Genomic dataset analyses require multiple methods of quality assessment to ensure that the data are appropriate for answering the biology question of interest. @@ -64,23 +59,20 @@ material: - title: "ChIP-seq Galaxy Workshop" type: "tutorial" + enable: "false" name: "chip-seq" zenodo_link: "" galaxy_tour: "" hands_on: "github" slides: "no" - questions: - "" - "" - objectives: - "" - "" - "" - time_estimation: "" - key_points: - "" - "" diff --git a/topics/dev/metadata.yaml b/topics/dev/metadata.yaml index 1728e53e..7c8fa57a 100644 --- a/topics/dev/metadata.yaml +++ b/topics/dev/metadata.yaml @@ -18,18 +18,14 @@ material: galaxy_tour: "" hands_on: "no" slides: "yes" - questions: - "" - "" - objectives: - "" - "" - "" - time_estimation: "1d/3h/6h" - key_points: - "" - "" @@ -44,21 +40,17 @@ material: hands_on: "external" hands_on_url: "http://planemo.readthedocs.io/en/latest/writing_standalone.html" slides: "yes" - 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" - time_estimation: "6h" - key_points: - "Galaxy Tool Syntax" - "Use Planemo" @@ -74,20 +66,16 @@ material: galaxy_tour: "" hands_on: "no" slides: "yes" - 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" - time_estimation: "3h" - key_points: - "Use Planemo" - "Contribute to the Main Tool Shed" @@ -99,23 +87,18 @@ material: galaxy_tour: "" hands_on: "no" slides: "yes" - 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" - time_estimation: "3h" - key_points: - "An Interactive Tour is easy to create: just a yaml file to fill" - "Use the Developper Tools of find the JQuery Selector" - "Help yourself by using the available web plugins and record an interactive tour" - - title: "Galaxy Interactive Environments" type: "tutorial" @@ -124,23 +107,18 @@ material: galaxy_tour: "" hands_on: "no" slides: "yes" - questions: - "What are Galaxy Interactive Environments (GIEs)?" - "How to enable GIEs in Galaxy?" - "How to develop your own GIE?" - objectives: - "Implement a Hello-World Galaxy Interactive Environment" - requirements: - title: "Docker basics" type: "external" link: "" - time_estimation: "1.5h" - key_points: - "Interactive Environments offer access to third-party applications within Galaxy" - "Interactive Environments run in a docker images for sandboxing and easy dependency management" @@ -150,19 +128,14 @@ material: name: "visualization-charts" hands_on: "yes" slides: "yes" - questions: - "How can I make a custom plugin for Charts?" - objectives: - "Learn how to add custom javascript plugins to the Galaxy Charts framework" - time_estimation: "1h" - key_points: - "Charts is a pluggable extension system for JS-only visualisations" - "With only 3 files we can integrate any JS-only visualizations into Galaxy" - - title: "Galaxy Webhooks" type: "tutorial" @@ -192,29 +165,22 @@ material: galaxy_tour: "" hands_on: "yes" slides: "yes" - questions: - "How can visualization plugins benefit science?" - objectives: - "Implement a first Galaxy visualization" - "Understand the client side vs. server side principle" - requirements: - title: "Javascript knowledge" type: "external" link: "" - time_estimation: "1.5h" - key_points: - "Visualizations require a different way of thinking: server and client side; downloading files rather than system level access" - "Interactivity is what makes visualizations different from static tools" - "Requires understanding of both the Galaxy ecosystem as well as HTML5/JS" - "Performance is more important than for static Galaxy tools" - - - title: "BioBlend module, a Python library to use Galaxy API" type: "tutorial" @@ -223,30 +189,24 @@ material: galaxy_tour: "" hands_on: "no" slides: "yes" - questions: - "What is the use of BioBlend?" - "How to use Galaxy through command line?" - objectives: - "Get familiar with BioBlend using IPython" - "Launch a Galaxy job / Visualize your actions with Galaxy" - "Launch a Galaxy workflow / Visualize your actions with Galaxy" - requirements: - title: "IPython" type: "external" link: "https://ipython.org" - time_estimation: "2h" - key_points: - "Play with IPython" - "Understand the job launching in Galaxy with BioBlend" - "Understand the workflow launching in Galaxy with BioBlend" - "Be able to adapt this knowledge to personal workflows" - - title: "Tool Dependencies and Conda" type: "tutorial" @@ -256,7 +216,6 @@ material: hands_on: "external" hands_on_url: "http://planemo.readthedocs.io/en/latest/writing_standalone.html" slides: "yes" - questions: - "How can I connect tools to applications and libraries?" - "What are the advantages of declaring dependencies for my tool?" @@ -264,20 +223,16 @@ material: - "What are Conda recipes and environments?" - "How do I find and use existing Conda recipes?" - "How do I develop Conda recipes for use within Galaxy tools?" - objectives: - "Learn to use existing Conda recipes to enable best practice tool dependency management in Galaxy." - "Learn the basics of building Conda recipes and contributing to Bioconda." - "Learn to use Planemo to assist in developing Galaxy tools from existing and new Conda recipes." - time_estimation: "1.25h" - requirements: - title: "Tool development and integration into Galaxy" type: "internal" link: "/topics/dev/tutorials/tool-integration/slides.html" - key_points: - "Conda and Bioconda are Galaxy best practices for connecting Galaxy tools to underlying applications and libraries." - "Leveraging Conda allows easy installation of your tool's dependencies by Galaxy deployers." @@ -285,7 +240,6 @@ material: - "Conda recipe skeletons, `conda build`, and with `planemo conda_install --conda_use_local` allow easy development of new Conda recipes at the same time as Galaxy tools that wrap them." - "Bioconda is a Galaxy best practice Conda channel for recipe publication." - "Bioconda has easy to follow contribution guidelines and is very welcoming to new contributors." - - title: "Tool Dependencies and Containers" type: "tutorial" @@ -295,31 +249,25 @@ material: hands_on: "external" hands_on_url: "http://planemo.readthedocs.io/en/latest/writing_standalone.html" slides: "yes" - questions: - "What are the advantages of running my Galaxy tool inside of a container?" - "How does Galaxy find a container to run my tool in?" - "What are BioContainers and how are they related to Galaxy?" - objectives: - "Explore the differences between containerizing Galaxy and tool execution." - "Discuss the advantages of containerizing tools." - "Learn to build best practice tools ready to be containerized." - time_estimation: "45m" - requirements: - title: "Tool development and integration into Galaxy" type: "internal" link: "/topics/dev/tutorials/tool-integration/slides.html" - key_points: - "It is becoming easier, more advantageous, and more common for Galaxy admins to run all tools within their own container." - "You can explicitly define a container for your tool - but it is easier and more reproducible to let Galaxy find or build one using your tool's best practice requirements." - "The Galaxy community will infrastructure to automatically build and/or publish containers for your tool as long as it defines best practice Conda dependencies." - "Planemo makes it easy to test your tool inside of containers." - - title: "Galaxy Code Architecture" type: "tutorial" @@ -327,19 +275,15 @@ material: zenodo_link: "" galaxy_tour: "" slides: "yes" - questions: - "How is the Galaxy code structured?" - "What do the various other projects related to Galaxy do?" - "What happens when I start Galaxy?" - objectives: - "Explore various aspects of the Galaxy codebase." - "Understand the various top-level files and modules in Galaxy." - "Understand how dependencies work in Galaxy's frontend and backend." - time_estimation: "2.5h" - requirements: [] key_points: - "Galaxy runs out of the box and fetches all needed dependencies." diff --git a/topics/epigenetics/metadata.yaml b/topics/epigenetics/metadata.yaml index acc7ed43..ba0fbe46 100644 --- a/topics/epigenetics/metadata.yaml +++ b/topics/epigenetics/metadata.yaml @@ -33,18 +33,14 @@ material: hands_on: "yes" slides: "no" edam_ontology: "topic_3173" - questions: - "What is methylation and why it cannot be recognised by a normal NGS procedure?" - "Can a different methylation influence the expression of a gene? How?" - "Which tools you can use to analyse methylation data?" - objectives: - "Learn how to analyse methylation data" - "Get a first intuition what are common pitfalls." - time_estimation: "3h" - key_points: - "The output of a methylation NGS is having a different distribution of the four bases. This is caused by the bisulfite treatment of the DNA." - "If there is a different level of methylation in the loci of a gene this can be a hint that something is wrong." diff --git a/topics/metagenomics/metadata.yaml b/topics/metagenomics/metadata.yaml index fb4181b4..0ebba03e 100644 --- a/topics/metagenomics/metadata.yaml +++ b/topics/metagenomics/metadata.yaml @@ -15,7 +15,6 @@ material: - title: "Introduction" type: "introduction" - slides: "yes" - title: "16S Microbial Analysis with Mothur" type: "tutorial" @@ -24,21 +23,16 @@ material: galaxy_tour: hands_on: "yes" slides: "no" - questions: - "What is the effect of normal variation in the gut microbiome on host health?" - objectives: - "Analyze of 16S rRNA sequencing data using the Mothur toolsuite in Galaxy" - time_estimation: "3-4h" - key_points: - "16S rRNA gene sequencing analysis results depend on the many algorithms used and their settings" - "Quality control and cleaning of your data is a crucial step in order to obtain optimal results" - "Adding a mock community to serve as a control sample can help you asses the error rate of your experimental setup" - "We can explore alpha and beta diversities using Krona and Phinch for dynamic visualizations" - - title: "Analyses of metagenomics data - The global picture" type: "tutorial" diff --git a/topics/sequence-analysis/metadata.yaml b/topics/sequence-analysis/metadata.yaml index 4aa76628..e73fe932 100644 --- a/topics/sequence-analysis/metadata.yaml +++ b/topics/sequence-analysis/metadata.yaml @@ -72,25 +72,6 @@ material: - "Second take home message" - "Third take home message" - - title: "small RNA" - type: "tutorial" - name: "srna" - zenodo_link: "url to Zenodo with input data" - galaxy_tour: "" - hands_on: "yes" - slides: "no" - questions: - - "First question addressed during the tutorial" - - "Second question addressed during the tutorial" - objectives: - - "First learning objectives of the tutorial" - - "Second learning objectives of the tutorial" - time_estimation: "1h/1d" - key_points: - - "First take home message" - - "Second take home message" - - "Third take home message" -- title: "RAD-Seq Reference-based data analysis" type: "tutorial" name: "ref-based-rad-seq" @@ -118,17 +99,13 @@ material: galaxy_tour: "de-novo-rad-seq" hands_on: "yes" slides: "no" - questions: - "How to analyze RAD sequencing data without a reference genome for a population genomics study?" - objectives: - "Analysis of RAD sequencing data without a reference genome" - "SNP calling from RAD sequencing data" - "Calculate population genomics statistics from RAD sequencing data" - time_estimation: "1/2d" - key_points: - "Simple sentence to sum up the first key point of the tutorial (Take home message)" - "Second key point" @@ -142,17 +119,13 @@ material: galaxy_tour: "genetic-map-rad-seq" hands_on: "yes" slides: "no" - questions: - "How to analyze RAD sequencing data for a genetic map study?" - objectives: - "SNP calling from RAD sequencing data" - "Find and correct haplotypes" - "Create input files for genetic map building software" - time_estimation: "1/2d" - key_points: - "Simple sentence to sum up the first key point of the tutorial (Take home message)" - "Second key point" diff --git a/topics/sequence-analysis/tutorials/srna/workflows/sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.ga b/topics/sequence-analysis/tutorials/srna/workflows/sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.ga deleted file mode 100644 index 526b6ad6..00000000 --- a/topics/sequence-analysis/tutorials/srna/workflows/sRNA_seq_Step_1_Read_preprocessing_and_removal_of_artifacts.ga +++ /dev/null @@ -1,1073 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "This workflow completes the first part of the small RNA-seq tutorial from read pre-processing to trimming.e", - "format-version": "0.1", - "name": "sRNA-seq Step 1: Read pre-processing and removal of artifacts (no grooming)", - "steps": { - "0": { - "annotation": "", - "content_id": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - 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"tool_version": "1.1.0", - "type": "tool", - "uuid": "cfb839fd-3e47-45bc-a653-25084172d2f0", - "workflow_outputs": [] - } - }, - "uuid": "25776284-5f81-42f9-9eb3-5b2fe5fa6db3" -} diff --git a/topics/training/metadata.yaml b/topics/training/metadata.yaml index 97613827..ed8f0614 100644 --- a/topics/training/metadata.yaml +++ b/topics/training/metadata.yaml @@ -6,130 +6,125 @@ requirements: docker_image: tutorial_galaxy_instance: material: - - - title: "Introduction" - type: "introduction" - slides: "yes" - - - - title: "Creating a new tutorial - Writing content in markdown" - type: "tutorial" - name: "create-new-tutorial-content" - zenodo_link: "" - galaxy_tour: "" - hands_on: "yes" - slides: "no" - questions: - - "How to integrate a new tutorial?" - - "How to write a tutorial with hands-on?" - objectives: - - "Creating a tutorial from scratch" - - "Creating hands-on" - time_estimation: "15min" - key_points: - - "Finding good training datasets is hard!" - - "You can highlight questions, tools and hints with a special syntax" - - "Self-learning can be done by questions and hidden answers" - - - - title: "Creating a new tutorial - Defining metadata" - type: "tutorial" - name: "create-new-tutorial-metadata" - zenodo_link: "" - galaxy_tour: "" - hands_on: "yes" - slides: "no" - questions: - - "What does Metadata in GTN means?" - - "Which kind of metadata can I annotate?" - - "For what is metadata used?" - objectives: - - "Adding metadata for a tutorial" - - "Defining learning objectives" - time_estimation: "15min" - key_points: - - "Metadata are useful to find the tutorial and generate the webpage" - - "Learning objectives, time estimation and other pedagogic metadata are helpful for the instructors" - - "Learning objectives and other pedagogic metadata should be filled before starting developing the tutorial to know where to go" - - - - title: "Creating a new tutorial - Setting up the infrastructure" - type: "tutorial" - name: "create-new-tutorial-jekyll" - zenodo_link: - galaxy_tour: - hands_on: "yes" - slides: "no" - questions: - - "How to setup the infrastructure to build training webpages?" - objectives: - - "Installing packages needed for rendering the webpage" - - "Running the GTN website locally" - - "Tracking changes to the content live in the webbrowser" - time_estimation: "15min" - key_points: - - "Checking the generated website can be done locally" - - - - title: "Creating a new tutorial - Creating Interactive Galaxy Tours" - type: "tutorial" - name: "create-new-tutorial-tours" - zenodo_link: "" - galaxy_tour: "" - hands_on: "yes" - slides: "no" - questions: - - "What is a Interactive Galaxy Tour?" - - "How can we create an Interactive Tour?" - objectives: - - "Creating a Galaxy tour from scratch" - - "Deploying and running a tour" - time_estimation: "15min" - key_points: - - "The Interactive Tours are a good training object for self-learning at its own speed" - - "It is now easy to create an Interactive Tour and test it" - - - - title: "Creating a new tutorial - Building a Docker flavor for a tutorial" - type: "tutorial" - name: "create-new-tutorial-docker" - zenodo_link: "" - galaxy_tour: "" - hands_on: "yes" - slides: "no" - questions: - - "How can we define the technical infrastructure for a tutorial?" - - "How to define the tools needed for a tutorial?" - - "How to add the needed data directly in an instance?" - - "How to add the workflows related to a tutorial?" - - "How can we check the technical infrastructure is working?" - objectives: - - "Creating a Galaxy Docker flavor with the needed tools, data and workflows for a tutorial" - - "Testing the Galaxy Docker flavor of a tutorial" - time_estimation: "30min" - key_points: - - "Tools, data and workflows can be easily integrated in a Docker flavor to have a useful technical support for a tutorial" - - "A Galaxy Docker flavor is a great support for training" - - "A Galaxy Docker flavor can be deployed 'anywhere' and is scalable" +- + title: "Introduction" + type: "introduction" + slides: "yes" +- + title: "Creating a new tutorial - Writing content in markdown" + type: "tutorial" + name: "create-new-tutorial-content" + zenodo_link: "" + galaxy_tour: "" + hands_on: "yes" + slides: "no" + questions: + - "How to integrate a new tutorial?" + - "How to write a tutorial with hands-on?" + objectives: + - "Creating a tutorial from scratch" + - "Creating hands-on" + time_estimation: "15min" + key_points: + - "Finding good training datasets is hard!" + - "You can highlight questions, tools and hints with a special syntax" + - "Self-learning can be done by questions and hidden answers" +- + title: "Creating a new tutorial - Defining metadata" + type: "tutorial" + name: "create-new-tutorial-metadata" + zenodo_link: "" + galaxy_tour: "" + hands_on: "yes" + slides: "no" + questions: + - "What does Metadata in GTN means?" + - "Which kind of metadata can I annotate?" + - "For what is metadata used?" + objectives: + - "Adding metadata for a tutorial" + - "Defining learning objectives" + time_estimation: "15min" + key_points: + - "Metadata are useful to find the tutorial and generate the webpage" + - "Learning objectives, time estimation and other pedagogic metadata are helpful for the instructors" + - "Learning objectives and other pedagogic metadata should be filled before starting developing the tutorial to know where to go" +- + title: "Creating a new tutorial - Setting up the infrastructure" + type: "tutorial" + name: "create-new-tutorial-jekyll" + zenodo_link: + galaxy_tour: + hands_on: "yes" + slides: "no" + questions: + - "How to setup the infrastructure to build training webpages?" + objectives: + - "Installing packages needed for rendering the webpage" + - "Running the GTN website locally" + - "Tracking changes to the content live in the webbrowser" + time_estimation: "15min" + key_points: + - "Checking the generated website can be done locally" +- + title: "Creating a new tutorial - Creating Interactive Galaxy Tours" + type: "tutorial" + name: "create-new-tutorial-tours" + zenodo_link: "" + galaxy_tour: "" + hands_on: "yes" + slides: "no" + questions: + - "What is a Interactive Galaxy Tour?" + - "How can we create an Interactive Tour?" + objectives: + - "Creating a Galaxy tour from scratch" + - "Deploying and running a tour" + time_estimation: "15min" + key_points: + - "The Interactive Tours are a good training object for self-learning at its own speed" + - "It is now easy to create an Interactive Tour and test it" +- + title: "Creating a new tutorial - Building a Docker flavor for a tutorial" + type: "tutorial" + name: "create-new-tutorial-docker" + zenodo_link: "" + galaxy_tour: "" + hands_on: "yes" + slides: "no" + questions: + - "How can we define the technical infrastructure for a tutorial?" + - "How to define the tools needed for a tutorial?" + - "How to add the needed data directly in an instance?" + - "How to add the workflows related to a tutorial?" + - "How can we check the technical infrastructure is working?" + objectives: + - "Creating a Galaxy Docker flavor with the needed tools, data and workflows for a tutorial" + - "Testing the Galaxy Docker flavor of a tutorial" + time_estimation: "30min" + key_points: + - "Tools, data and workflows can be easily integrated in a Docker flavor to have a useful technical support for a tutorial" + - "A Galaxy Docker flavor is a great support for training" + - "A Galaxy Docker flavor can be deployed 'anywhere' and is scalable" +- + title: "Good practices to run a workshop" + type: "tutorial" + name: "good-practices" + zenodo_link: "" + galaxy_tour: "" + hands_on: "no" + slides: "yes" + questions: + - "What do we need to take care when running a workshop?" + - "What are the good practices?" + objectives: + - "Reflect on the things to do before, during and after a workshop" + time_estimation: "1h/1d" + key_points: + - "Prepare your workshop" + - "Take care of your trainees" - - - title: "Good practices to run a workshop" - type: "tutorial" - name: "good-practices" - zenodo_link: "" - galaxy_tour: "" - hands_on: "no" - slides: "yes" - questions: - - "What do we need to take care when running a workshop?" - - "What are the good practices?" - objectives: - - "Reflect on the things to do before, during and after a workshop" - time_estimation: "1h/1d" - key_points: - - "Prepare your workshop" - - "Take care of your trainees" maintainers: - name: "Bérénice Batut" diff --git a/topics/training/tutorials/create-new-tutorial-metadata/tutorial.md b/topics/training/tutorials/create-new-tutorial-metadata/tutorial.md index 4337c8a0..97532f15 100644 --- a/topics/training/tutorials/create-new-tutorial-metadata/tutorial.md +++ b/topics/training/tutorials/create-new-tutorial-metadata/tutorial.md @@ -39,6 +39,7 @@ The first file we will fill is the `metadata.yaml` file describing the metadata - `title`: title of the tutorial - `type: "tutorial"` +- `enable`: `"true"` to make your tutorial accessible via the topic page or `"false"` otherwise - `name`: name of the tutorial (name of the subdirectory where the files related to the tutorial will be stored) - `zenodo_link`: link on Zenodo to the input data for the tutorial (not ideal but it can be empty) - `galaxy_tour`: name of the galaxy tour diff --git a/topics/usegalaxy/metadata.yaml b/topics/usegalaxy/metadata.yaml index 277da23f..a182d08d 100644 --- a/topics/usegalaxy/metadata.yaml +++ b/topics/usegalaxy/metadata.yaml @@ -140,6 +140,7 @@ material: key_points: requirements: references: "" + maintainers: - name: "Anton Nekrutenko" diff --git a/topics/variant-analysis/metadata.yaml b/topics/variant-analysis/metadata.yaml index fd86fe16..64cd26ec 100644 --- a/topics/variant-analysis/metadata.yaml +++ b/topics/variant-analysis/metadata.yaml @@ -26,6 +26,7 @@ material: - title: "Variant calling: Diploid case" type: "tutorial" + enable: "false" name: "diploid-variant-calling" zenodo_link: "" galaxy_tour: ""