diff --git a/_includes/pathway-card.html b/_includes/pathway-card.html new file mode 100644 index 00000000000000..88f1f1553e84f7 --- /dev/null +++ b/_includes/pathway-card.html @@ -0,0 +1,32 @@ +{% assign path = include.path %} + +{% assign coverimage = path.coverimage | default: "/assets/images/GTNLogo1000.png" %} +{% assign coverimagealt = path.coverimagealt | default: "GTN logo with a multi-coloured star and the words Galaxy Training Network"%} + + +
+ +
+
+ {% if path.cover-image %} + {{ path.cover-image-alt }} + {% else %} + {{ coverimagealt }} + {% endif %} +
+
+
{{path.title}}
+

+ {{path.description}} +

+
+ +
+
+
+ + diff --git a/assets/css/main.scss b/assets/css/main.scss index 60c34d713be902..5182e644b148ea 100644 --- a/assets/css/main.scss +++ b/assets/css/main.scss @@ -572,7 +572,7 @@ blockquote { } } -.pathway{ +.pathwaylist{ display: flex; flex-wrap: wrap; flex-direction: row; @@ -580,19 +580,32 @@ blockquote { margin-bottom: 2rem; .pathwayitem { - width: 100%; background: transparent; - border: 1px solid var(--border-light); + + .card{ + margin-bottom: 1em; + } + .card-body{ + height: 17rem; + overflow: hidden; + } + .card-text{ + margin: 1rem; + vertical-align: center; + } + .card-title{ + height: 5rem; + } .card-header { - background: var(--brand-color); - border-bottom: 1px solid var(--border-light); + background: var(--brand-color); + border-bottom: 1px solid var(--border-light); } } .pathwaycover { width: 100%; - object-fit: cover; - margin-top: auto; - margin-bottom: auto; + max-height: 100%; + object-fit: contain; + margin-top: 1em; background-color: white; border-radius: 2rem;; padding: 1rem; diff --git a/assets/images/galaxy-e-logo.png b/assets/images/galaxy-e-logo.png new file mode 100644 index 00000000000000..3273403080ee94 Binary files /dev/null and b/assets/images/galaxy-e-logo.png differ diff --git a/assets/images/microgalaxy-logo.png b/assets/images/microgalaxy-logo.png new file mode 100644 index 00000000000000..ea12683deefd15 Binary files /dev/null and b/assets/images/microgalaxy-logo.png differ diff --git a/learning-pathways/admin-training.md b/learning-pathways/admin-training.md index 4eacfc64183a50..46d484b6124196 100644 --- a/learning-pathways/admin-training.md +++ b/learning-pathways/admin-training.md @@ -1,6 +1,7 @@ --- layout: learning-pathway title: Admin Training Course +type: admin-dev description: | Learn how to setup, configure, and maintain your own Galaxy server. This learning pathway will guide you through all the steps required to setup your own Galaxy server with Ansible, diff --git a/learning-pathways/genome-annotation-eukaryote.md b/learning-pathways/genome-annotation-eukaryote.md index d08c3f2b6fa6d2..90c64b03306db7 100644 --- a/learning-pathways/genome-annotation-eukaryote.md +++ b/learning-pathways/genome-annotation-eukaryote.md @@ -3,6 +3,7 @@ layout: learning-pathway title: Genome annotation for eukaryotes description: | Learn how to annotate an eukaryotic genome sequence: identify repeated regions, find the position and function of genes, and even set up a manual curation environment with Apollo. +type: use tags: [genome annotation, eukaryote] cover-image: assets/images/gga.png @@ -12,6 +13,8 @@ editorial_board: funding: - erasmusplus + + pathway: - section: "Module 1: Introduction" description: | diff --git a/learning-pathways/genome-annotation-prokaryote.md b/learning-pathways/genome-annotation-prokaryote.md index 484b1ebac9080c..57fb30b68a0b04 100644 --- a/learning-pathways/genome-annotation-prokaryote.md +++ b/learning-pathways/genome-annotation-prokaryote.md @@ -3,6 +3,7 @@ layout: learning-pathway title: Genome annotation for prokaryotes description: | Learn how to annotate a prokaryotic genome sequence: find the position and function of genes, and even set up a manual curation environment with Apollo. +type: use tags: [genome annotation, prokaryote] cover-image: assets/images/gga.png diff --git a/learning-pathways/index.md b/learning-pathways/index.md index 16b4311a4b24cd..8c52972c511538 100644 --- a/learning-pathways/index.md +++ b/learning-pathways/index.md @@ -2,46 +2,40 @@ layout: page --- -{% assign pathways = site.pages | where: "layout", "learning-pathway" | sort: "priority", "last" %} +{% assign pathways_science = site.pages | where: "layout", "learning-pathway" | where: "type", "use" | sort: "priority", "last" %} + +{% assign pathways_other = site.pages | where: "layout", "learning-pathway" | where_exp: "item", "item.type != 'use'" | sort: "priority", "last" %} # Learning Pathways Learning pathways are sets of tutorials curated for you by community experts to form a coherent set of lessons around a topic, building up knowledge as you go. We always recommend to follow the tutorials in the order they are listed in the pathway. +## For Scientists + + -
-{% for path in pathways %} - -{% assign coverimage = path.coverimage | default: "/assets/images/GTNLogo1000.png" %} -{% assign coverimagealt = path.coverimagealt | default: "GTN logo with a multi-coloured star and the words Galaxy Training Network"%} -
- -
-
- {% if path.cover-image %} - {{ path.cover-image-alt }} - {% else %} - {{ coverimagealt }} - {% endif %} -
-
-
-

- {% for tag in path.tags %} - {{ tag }} - {% endfor %} -
-

- {{ path.description }} -

- View Learning Pathway -
-
-
+
+ + +{% for path in pathways_science %} + +{% include _includes/pathway-card.html path=path %} + +{% endfor %} +
+ +## For Teachers, Developers and System Administrators + + +
+ +{% for path in pathways_other %} + +{% include _includes/pathway-card.html path=path %} + {% endfor %} +
diff --git a/learning-pathways/intro-to-galaxy-and-ecology.md b/learning-pathways/intro-to-galaxy-and-ecology.md index 9d777033b81622..35fd4168c1d621 100644 --- a/learning-pathways/intro-to-galaxy-and-ecology.md +++ b/learning-pathways/intro-to-galaxy-and-ecology.md @@ -1,17 +1,23 @@ --- layout: learning-pathway +type: use + +title: Introduction to Galaxy and Ecological data analysis +description: | + This learning path aims to teach you the basics of Galaxy and analysis of ecological data. + You will learn how to use Galaxy for analysis, and will be guided through the common + steps of biodiversity data analysis: download, check, filter and explore biodiversity data and analyze abundance data through modeling. + + tags: [beginner] +cover-image: assets/images/galaxy-e-logo.png +cover-image-alt: "Drawing of an Ecological System" editorial_board: - yvanlebras funding: - erasmusplus -title: Introduction to Galaxy and Ecological data analysis -description: | - This learning path aims to teach you the basics of Galaxy and analysis of ecological data. - You will learn how to use Galaxy for analysis, and will be guided through the common - steps of biodiversity data analysis: download, check, filter and explore biodiversity data and analyze abundance data through modeling. pathway: - section: "Module 1: Introduction to Galaxy" diff --git a/learning-pathways/intro-to-galaxy-and-genomics.md b/learning-pathways/intro-to-galaxy-and-genomics.md index 7fd728542d87b8..35519493954880 100644 --- a/learning-pathways/intro-to-galaxy-and-genomics.md +++ b/learning-pathways/intro-to-galaxy-and-genomics.md @@ -1,6 +1,7 @@ --- layout: learning-pathway tags: [beginner] +type: use editorial_board: - shiltemann diff --git a/learning-pathways/intro-to-r-and-ml.md b/learning-pathways/intro-to-r-and-ml.md index ade4c4a05b15f8..ef9eb1283a47df 100644 --- a/learning-pathways/intro-to-r-and-ml.md +++ b/learning-pathways/intro-to-r-and-ml.md @@ -1,6 +1,7 @@ --- layout: learning-pathway tags: [beginner] +type: use editorial_board: - fpsom diff --git a/learning-pathways/metagenomics.md b/learning-pathways/metagenomics.md index 3a9c5d8a5ec3c0..b9e5318a0b828c 100644 --- a/learning-pathways/metagenomics.md +++ b/learning-pathways/metagenomics.md @@ -1,5 +1,8 @@ --- layout: learning-pathway # (uncomment this line to activate it) +type: use +cover-image: assets/images/microgalaxy-logo.png +cover-image-alt: "microgalaxy logo" editorial_board: - bebatut @@ -54,7 +57,7 @@ pathway: description: | This module covers the following questions: - Which species (or genera, families, ...) are present in my sample? - - What are the different approaches and tools to get the community profile of my sample? + - What are the different approaches and tools to get the community profile of my sample? - How can we visualize and compare community profiles? This module will cover taxonomic profiling in theory and also with an example tutorial. @@ -67,15 +70,15 @@ pathway: #description: Application tutorial #- section: "Module 6: Taxonomic binning" - # description: + # description: # # tutorials: # - name: learner_participation_engagement # topic: metagenomics - + #- section: "Module 7: Community Biodiversity" - # description: + # description: # # tutorials: # - name: learner_participation_engagement diff --git a/learning-pathways/pathway-example.md b/learning-pathways/pathway-example.md index 97cea167d90549..3a6962741f4b9d 100644 --- a/learning-pathways/pathway-example.md +++ b/learning-pathways/pathway-example.md @@ -6,6 +6,8 @@ description: | Description of the pathway. What will be covered, what are the learning objectives, etc? Make this as thorough as possible, 1-2 paragraphs. This appears on the index page that lists all the learning paths, and at the top of the pathway page + +type: use # 'use' for science topics, or admin-dev or instructors tags: [some, keywords, here ] editorial_board: - shiltemann diff --git a/learning-pathways/train-the-trainers.md b/learning-pathways/train-the-trainers.md index 00e78e5c457111..f4530643664549 100644 --- a/learning-pathways/train-the-trainers.md +++ b/learning-pathways/train-the-trainers.md @@ -1,5 +1,6 @@ --- layout: learning-pathway # (uncomment this line to activate it) +type: instructors title: Train the Trainers description: | diff --git a/package-lock.json b/package-lock.json index ccc7c673d5e33a..98ae356d949d57 100644 --- a/package-lock.json +++ b/package-lock.json @@ -2186,9 +2186,9 @@ } }, "node_modules/make-dir/node_modules/semver": { - "version": "6.3.0", - "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.0.tgz", - "integrity": "sha512-b39TBaTSfV6yBrapU89p5fKekE2m/NwnDocOVruQFS1/veMgdzuPcnOM34M6CwxW8jH/lxEa5rBoDeUwu5HHTw==", + "version": "6.3.1", + "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.1.tgz", + "integrity": "sha512-BR7VvDCVHO+q2xBEWskxS6DJE1qRnb7DxzUrogb71CWoSficBxYsiAGd+Kl0mmq/MprG9yArRkyrQxTO6XjMzA==", "bin": { "semver": "bin/semver.js" } @@ -3287,9 +3287,9 @@ } }, "node_modules/semver": { - "version": "7.5.3", - "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.3.tgz", - "integrity": "sha512-QBlUtyVk/5EeHbi7X0fw6liDZc7BBmEaSYn01fMU1OUYbf6GPsbTtd8WmnqbI20SeycoHSeiybkE/q1Q+qlThQ==", + "version": "7.5.4", + "resolved": "https://registry.npmjs.org/semver/-/semver-7.5.4.tgz", + "integrity": "sha512-1bCSESV6Pv+i21Hvpxp3Dx+pSD8lIPt8uVjRrxAUt/nbswYc+tK6Y2btiULjd4+fnq15PX+nqQDC7Oft7WkwcA==", "dependencies": { "lru-cache": "^6.0.0" }, diff --git a/yarn.lock b/yarn.lock index e702311fbe7220..33b71b453a6ac6 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2176,14 +2176,14 @@ selenium-webdriver@4.3.0: ws ">=8.7.0" semver@^6.0.0: - version "6.3.0" - resolved "https://registry.yarnpkg.com/semver/-/semver-6.3.0.tgz#ee0a64c8af5e8ceea67687b133761e1becbd1d3d" - integrity sha512-b39TBaTSfV6yBrapU89p5fKekE2m/NwnDocOVruQFS1/veMgdzuPcnOM34M6CwxW8jH/lxEa5rBoDeUwu5HHTw== + version "6.3.1" + resolved "https://registry.yarnpkg.com/semver/-/semver-6.3.1.tgz#556d2ef8689146e46dcea4bfdd095f3434dffcb4" + integrity sha512-BR7VvDCVHO+q2xBEWskxS6DJE1qRnb7DxzUrogb71CWoSficBxYsiAGd+Kl0mmq/MprG9yArRkyrQxTO6XjMzA== semver@^7.3.4, semver@^7.3.5: - version "7.5.3" - resolved "https://registry.yarnpkg.com/semver/-/semver-7.5.3.tgz#161ce8c2c6b4b3bdca6caadc9fa3317a4c4fe88e" - integrity sha512-QBlUtyVk/5EeHbi7X0fw6liDZc7BBmEaSYn01fMU1OUYbf6GPsbTtd8WmnqbI20SeycoHSeiybkE/q1Q+qlThQ== + version "7.5.4" + resolved "https://registry.yarnpkg.com/semver/-/semver-7.5.4.tgz#483986ec4ed38e1c6c48c34894a9182dbff68a6e" + integrity sha512-1bCSESV6Pv+i21Hvpxp3Dx+pSD8lIPt8uVjRrxAUt/nbswYc+tK6Y2btiULjd4+fnq15PX+nqQDC7Oft7WkwcA== dependencies: lru-cache "^6.0.0"