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}} +

+
+
+ {% for tag in path.tags %} + {{ tag }} + {% endfor %} +
+
+ +
+ + 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 cc338b90969f0e..61fce4be9a50e4 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/climate-learning.md b/learning-pathways/climate-learning.md new file mode 100644 index 00000000000000..6caa00da78e405 --- /dev/null +++ b/learning-pathways/climate-learning.md @@ -0,0 +1,26 @@ +--- +layout: learning-pathway + +title: Discovering galaxy through climate analysis +description: | + How to have a complete overview of how Galaxy works going from the user welcome page to use batch tools and finishing by conducting interactive analysis. These set of 3 Climate tutorials allow you to understand and see plenty of the multiple features of Galaxy and learning about the cool subject of climate analysis. +tags: [Climate, Overview] + + +pathway: + - section: "Following 3 climate tutorials" + description: | + During this session you will first learn about the galaxy interface and how to use batch tools. Then, you'll be able to run through a jupyter notebook launch from Galaxy. Finally, you will conduct a climate analysis on a desktop application with Panoply. + tutorials: + - name: pangeo + topic: climate + - name: pangeo-notebook + topic: climate + - name: panoply + topic: climate + +--- + +This can be done in less than 3h. To be really complete you can then create a workflow from the history of your 1st tutorial and show how workflows work. + + diff --git a/learning-pathways/genome-annotation-eukaryote.md b/learning-pathways/genome-annotation-eukaryote.md index 2b2668b9b62d93..f27edf38d3961f 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 @@ maintainers: 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 e0b5ba98fc8d7e..3d98afb34c5419 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"%} -
-
-

{{path.title}}

 -
-
-
- {% 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 db636659bc8d2a..99e360ce1a60e0 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" maintainers: - 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 04a5839a4a340e..0ad675bd28147f 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 maintainers: - shiltemann diff --git a/learning-pathways/intro-to-r-and-ml.md b/learning-pathways/intro-to-r-and-ml.md index d5c9561c6f9daf..56749f657177b4 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 maintainers: - fpsom diff --git a/learning-pathways/metagenomics.md b/learning-pathways/metagenomics.md index 4a123cb724c9c3..e0071e35166514 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" maintainers: - 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 5a2319d0b04a36..f46507ffda7c60 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 ] cover-image: assets/images/gat.png # optional, define your own cover image for the pathway index page, default is the GTN logo diff --git a/learning-pathways/train-the-trainers.md b/learning-pathways/train-the-trainers.md index 348a2346f0a4f0..3e8de1f4cfa380 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/topics/admin/tutorials/backup-cleanup/tutorial.md b/topics/admin/tutorials/backup-cleanup/tutorial.md index 792d35b6dac5e8..92d9b2ce27e7b5 100644 --- a/topics/admin/tutorials/backup-cleanup/tutorial.md +++ b/topics/admin/tutorials/backup-cleanup/tutorial.md @@ -129,7 +129,7 @@ tutorial]({% link topics/admin/tutorials/gxadmin/tutorial.md %}). > + user: galaxy # Run as the Galaxy user > + minute: "0" > + hour: "0" -> + job: "GALAXY_LOG_DIR=/tmp/gxadmin/ GALAXY_ROOT={{ galaxy_root }}/server /usr/local/bin/gxadmin galaxy cleanup 60" +> + job: "SHELL=/bin/bash source {{ galaxy_venv_dir }}/bin/activate && GALAXY_LOG_DIR=/tmp/gxadmin/ GALAXY_ROOT={{ galaxy_root }}/server GALAXY_CONFIG_FILE={{ galaxy_config_file }} /usr/local/bin/gxadmin galaxy cleanup 60" > {% endraw %} > ``` > {: data-commit="Configure gxadmin to cleanup data"} diff --git a/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md b/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md index 99796b3d8881e3..36cd86755743db 100644 --- a/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md +++ b/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md @@ -1083,37 +1083,76 @@ We use **Heatmap w ggplot** tool along with other tabular manipulating tools to > Heatmap > - > 1. {% tool [Multi-Join](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1) %} with the following parameters: - > - {% icon param-file %} *"File to join"*: `VFs accessions` collection output of **cut** {% icon tool %} from the **Gene based Pathogentic Identification** section + > 1. {% tool [Collapse Collection](toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0) %} with the following parameters: + > - {% icon param-collection %} *"Collection of files to collapse into single dataset"*: `VFs accessions` collection output of **cut** {% icon tool %} from the **Gene based Pathogentic Identification** section + > - *"Prepend File name"*: `No` + > 2. {% tool [Add line to file](toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0) %} with the following parameters: + > - {% icon param-file %} *"input file"*: `VFs accessions` output from **Collapse Collection** {% icon tool %} + > - *"text to add"*: `All_VFs` + > 3. {% tool [Multi-Join](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1) %} with the following parameters: + > - {% icon param-file %} *"File to join"*: `VFs accessions` output from **Add line to file** {% icon tool %} > - {% icon param-file %} *"add additional file"*: `VFs accessions with SampleID` collection output of **Add line to file** {% icon tool %} from the **Gene based Pathogentic Identification** section > - *"Common key column"*: `1` > - *"Column with values to preserve"*: `Column: 1` > - *"Add header line to the output file"*: `Yes` > - *"Input files contain a header line (as first line)"*: `Yes` > - *"Ignore duplicated keys"*: `Yes` - > - > 2. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4) %} with the following parameters: + > 4. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4) %} with the following parameters: > - {% icon param-file %} *"File to process"*: output of **Multi-Join** {% icon tool %} > - In *"Find and Replace"*: > - {% icon param-repeat %} *"Insert Find and Replace"* - > - *"Find pattern"*: `^[^0]\w+` - > - *"Replace with"*: `1` + > - *"Find pattern"*: `dataset_(.*?)_` + > - *"Replace with"*: `Sample_` > - *"Find-Pattern is a regular expression"*: `Yes` > - *"Replace all occurences of the pattern"*: `Yes` + > - *"Ignore first line"*: `No` + > - *"Find and Replace text in"*: `entire line` + > - {% icon param-repeat %} *"Insert Find and Replace"* + > - *"Find pattern"*: `(\S+)` + > - *"Replace with"*: `Acc_$1` + > - *"Find-Pattern is a regular expression"*: `Yes` + > - *"Case-Insensitive search"*: `Yes` + > - *"Replace all occurences of the pattern"*: `Yes` > - *"Ignore first line"*: `Yes` - > - *"Find and Replace text in"*: `specific column` - > - *"in column*": `Column: 2` - > 3. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4) %} with the following parameters: + > - *"Find and Replace text in"*: `entire line` + > 5. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4) %} with the following parameters: > - {% icon param-file %} *"File to process"*: output of **Replace** {% icon tool %} > - In *"Find and Replace"*: > - {% icon param-repeat %} *"Insert Find and Replace"* - > - *"Find pattern"*: `^[^0]\w+` + > - *"Find pattern"*: `Acc_0` + > - *"Replace with"*: `0` + > - *"Find-Pattern is a regular expression"*: `No` + > - *"Case-Insensitive search"*: `Yes` + > - *"Replace all occurences of the pattern"*: `Yes` + > - *"Ignore first line"*: `Yes` + > - *"Find and Replace text in"*: `entire line` + > 6. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4) %} with the following parameters: + > - {% icon param-file %} *"File to process"*: output of **Replace** {% icon tool %} + > - In *"Find and Replace"*: + > - {% icon param-repeat %} *"Insert Find and Replace"* + > - *"Find pattern"*: `Acc_\S*` > - *"Replace with"*: `1` > - *"Find-Pattern is a regular expression"*: `Yes` > - *"Replace all occurences of the pattern"*: `Yes` > - *"Ignore first line"*: `Yes` - > - *"Find and Replace text in"*: `specific column` - > - *"in column*": `Column: 3` + > - *"Case-Insensitive search"*: `No` + > - *"Find and Replace text in"*: `entire line` + > 7. {% tool [Advanced Cut](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0) %} with the following parameters: + > - {% icon param-file %} *"File to cut"*: output of **Multi-Join** {% icon tool %} + > - *"Operation"*:`Keep` + > - *"Delimited by"*:`Tab` + > - *"Cut by"*:`fields` + > - *"List of Fields"*:`1` + > 8. {% tool [Advanced Cut](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0) %} with the following parameters: + > - {% icon param-file %} *"File to cut"*: output of the last **Replace** {% icon tool %} + > - *"Operation"*:`Discard` + > - *"Delimited by"*:`Tab` + > - *"Cut by"*:`fields` + > - *"List of Fields"*:`1,2` + > 9. {% tool [Paste](Paste1) %} with the following parameters: + > - {% icon param-file %} *"Paste"*: output of **Advanced Cut** (Tool N. 7) {% icon tool %} + > - {% icon param-file %} *"and"*: output of **Advanced Cut** (Tool N. 8) {% icon tool %} + > - *"Delimit by"*:`Tab` {: .hands_on} 2. Draw heatmap 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"