Merge pull request #1 from vloux/proteome_annotation

Proteome annotation

.travis.yml

@@ -39,6 +39,7 @@ matrix:
 install:
   - sudo apt-get update
   - sudo update-ca-certificates
+  - sudo pip install awscli
   - make install-conda
   - export PATH="$HOME/miniconda3/bin:$PATH"
   - conda config --set always_yes yes --set changeps1 no
@@ -67,6 +68,7 @@ script:
       then
         make check-yaml
         make check-frontmatter
+        make check-workflows
       elif [ "$CHECK" == "slides" ]
       then
         make check-slides
@@ -87,4 +89,5 @@ after_success:
       make annotate
       make build
       bin/publish
+      bin/publish-archive
     fi

CONTRIBUTORS.yaml

@@ -23,6 +23,9 @@ abretaud:
     gitter: abretaud
     orcid: 0000-0003-0914-2470
 
+abdulrahmanazab:
+    name: Abdulrahman Azab
+
 afgane:
     name: Enis Afgan
 
@@ -129,6 +132,7 @@ dpryan79:
 
 dsobral:
     name: Daniel Sobral
+
 SanneAbeln:
     name: Sanne Abeln
 
@@ -171,6 +175,9 @@ frederikcoppens:
 friedue:
     name: Friederike Dündar
 
+gmauro:
+    name: Gianmauro Cuccuru
+
 guerler:
     name: Aysam Guerler
 
@@ -221,6 +228,9 @@ joachimwolff:
     name: Joachim Wolff
     email: [email protected]
 
+JovMaksimovic:
+    name: Jovana Maksimovic
+
 jpmaree:
 
 jraysajulga:
@@ -267,6 +277,9 @@ marziacremona:
     name: Marzia A Cremona
     email: [email protected]
 
+matthias313:
+    name: Matthias
+
 mblue9:
     name: Maria Doyle
 
@@ -321,18 +334,22 @@ odoppelt:
 pajanne:
     name: Anne Pajon
 
+pavanvidem:
+    name: Pavankumar Videm
+
 polkhe:
     name: Ekaterina Polkh
 
-pvanheus:
-    name: Peter van Heusden
-
 pratikdjagtap:
     name: Pratik Jagtap
     email: [email protected]
 
-pavanvidem:
-    name: Pavankumar Videm
+pravs3683:
+    name: Praveen Kumar
+    email: [email protected]
+
+pvanheus:
+    name: Peter van Heusden
 
 reginaesinamabotsi:
     name: Regina Esinam Abotsi
@@ -343,6 +360,9 @@ sanneabeln:
 sarah-peter:
     name: Sarah Peter
 
+Shians:
+    name: Shian Su
+
 shiltemann:
     name: Saskia Hiltemann
     maintainer_contact: gitter
@@ -401,6 +421,12 @@ vdda:
 vivekbhr:
     name: Vivek Bhardwaj
 
+vloux:
+    name: Valentin Loux
+    email : [email protected]
+    twitter: vloux
+    orcid: 0000-0002-8268-915X
+
 willdurand:
     name: William Durand
 
@@ -413,3 +439,6 @@ yhoogstrate:
 yvanlebras:
     name: Yvan Le Bras
     email: [email protected]
+    twitter: Yvan2935
+    gitter: yvanlebras
+    orcid: 0000-0002-8504-068X

Makefile

@@ -41,14 +41,14 @@ create-env: ## create conda environment
 	fi
 .PHONY: create-env
 
-ACTIVATE_ENV = source $(dir ${CONDA})activate ${CONDA_ENV}
+ACTIVATE_ENV = source $(shell dirname $(dir $(CONDA)))/bin/activate $(CONDA_ENV)
 
 install: clean ## install dependencies
 	$(ACTIVATE_ENV) && \
 		npm install decktape && \
 		gem update --system && \
 		gem install nokogiri:'1.10.0' -- --use-system-libraries --with-xml=$(CONDA_PREFIX)/lib && \
-		gem install jekyll-environment-variables awesome_bot html-proofer jekyll jekyll-feed pkg-config:'~> 1.1'
+		gem install addressable:'2.5.2' jekyll jekyll-feed jekyll-environment-variables jekyll-github-metadata jekyll-scholar csl-styles awesome_bot html-proofer pkg-config
 .PHONY: install
 
 serve: ## run a local server (You can specify PORT=, HOST=, and FLAGS= to set the port, host or to pass additional flags)
@@ -69,7 +69,7 @@ build: clean ## build files but do not run a server (You can specify FLAGS= to p
 check-frontmatter: build ## Validate the frontmatter
 	$(ACTIVATE_ENV) && \
 		find topics/ -name tutorial.md -or -name slides.html -or -name metadata.yaml | \
-	    xargs -n1 ruby bin/validate-frontmatter.rb 
+	    xargs -n1 ruby bin/validate-frontmatter.rb
 .PHONY: check-frontmatter
 
 check-html: build ## validate HTML
@@ -84,6 +84,11 @@ check-html: build ## validate HTML
 	      	./_site
 .PHONY: check-html
 
+check-workflows: build ## validate Workflows
+	$(ACTIVATE_ENV) && \
+		bash bin/validate-json.sh
+.PHONY: check-workflows
+
 check-html-internal: build ## validate HTML (internal links only)
 	$(ACTIVATE_ENV) && \
 		htmlproofer \
@@ -113,10 +118,10 @@ check-slides: build  ## check the markdown-formatted links in slides
 check-yaml: ## lint yaml files
 	$(ACTIVATE_ENV) && \
 		find . -name "*.yaml" | xargs -L 1 -I '{}' sh -c "yamllint {}" \
-		find topics -name '*.yml' | xargs -L 1 -I '{}' sh -c "yamllint {}" 
+		find topics -name '*.yml' | xargs -L 1 -I '{}' sh -c "yamllint {}"
 .PHONY: check-yaml
 
-check: check-yaml check-frontmatter check-html-internal check-html check-slides ## run all checks
+check: check-yaml check-frontmatter check-html-internal check-html check-slides check-workflows ## run all checks
 .PHONY: check
 
 check-links-gh-pages:  ## validate HTML on gh-pages branch (for daily cron job)

_config.yml

@@ -19,8 +19,8 @@ email: [email protected]
 description: A collection of tutorials generated and maintained by Galaxy Community Members across the world
 url: "https://galaxyproject.github.io/"
 baseurl: "/training-material"
-github_repository: "https://github.com/galaxyproject/training-material"
-github_organization_name: "galaxyproject"
+repository: galaxyproject/training-material
+repository_branch: "master"
 gitter_url: "https://gitter.im/Galaxy-Training-Network/Lobby"
 logo: "assets/images/GTN.png"
 small_logo: "assets/images/GTN-60px.png"
@@ -54,6 +54,14 @@ figurify:
   skip_titles:
     - Example of an image with a caption
 
+# Scholar
+scholar:
+  source: topics/
+  bibliography: "**/*.bib"
+  sort_by: "year,month"
+  bibliography_template: bibtemplate
+  style: g3
+
 # Icon tag config
 icon-tag:
   # in tutorials
@@ -93,6 +101,7 @@ icon-tag:
   galaxy-upload: fa fa-upload
   galaxy-chart-select-data: fa fa-database
   galaxy-save: fa fa-save
+  galaxy-scratchbook: fa fa-th
 
   # menus, links
   zenodo_link: fa-files-o
@@ -113,6 +122,7 @@ icon-tag:
   linkedin: fa-linkedin
   orcid: ai-orcid
   curriculum: fa-graduation-cap
+  hall-of-fame: fa-users
 
 # To exclude in _site
 exclude:
@@ -143,4 +153,6 @@ include:
 plugins:
   - jekyll-feed
   - jekyll-environment-variables
+  - jekyll-github-metadata
+  - jekyll-scholar
 

_includes/default-header.html

@@ -12,7 +12,12 @@
             <div class="collapse navbar-collapse" id="top-navbar">
                 <ul class="navbar-nav">
                     <li class="nav-item">
-                        <a class="nav-link" href="{{ site.github_repository }}" title="View on GitHub">
+                         <a class="nav-link" href="{{ site.baseurl }}/hall-of-fame" title="Hall of Fame">
+                            {% icon hall-of-fame %} Contributors
+                        </a>
+                    </li>
+                    <li class="nav-item">
+                        <a class="nav-link" href="{{ site.github.repository_url }}" title="View on GitHub">
                             {% icon github %} View on GitHub
                         </a>
                     </li>

_includes/material.jsonld

@@ -1,2 +1,4 @@
 {% assign material = include.material %}
-{{ material | to_jsonld }}
+{% assign topic = include.topic %}
+{% assign site = include.site %}
+{{ material | to_jsonld: topic, site }}

_layouts/base.html

@@ -18,6 +18,7 @@
         </script>
         {% endif %}
         <link rel="stylesheet" href="{{ "/assets/css/bootstrap.min.css?v=3" | prepend: site.baseurl }}">
+        <link rel="stylesheet" href="{{ "/assets/css/bootstrap-toc.min.css" | prepend: site.baseurl }}">
         <link rel="stylesheet" href="{{ "/assets/css/main.css?v=2" | prepend: site.baseurl }}">
         <link rel="stylesheet" href="{{ "/assets/css/font-awesome.css" | prepend: site.baseurl }}">
         <link rel="stylesheet" href="{{ "/assets/css/academicons.css" | prepend: site.baseurl }}">
@@ -38,13 +39,14 @@
         <meta property="og:description" content="{{ og_desc | strip_html | truncate: 60}}" />
         <meta property="og:image" content="{{ "/assets/images/GTNLogo1000.png" | prepend: site.baseurl }}" />
     </head>
-    <body>
+    <body data-spy="scroll" data-target="#toc">
         {{ content }}
     </body>
     <script type="text/javascript" src="{{ "/assets/js/jquery.slim.min.js" | prepend: site.baseurl }}"></script>
     <script type="text/javascript" src="{{ "/assets/js/popper.min.js" | prepend: site.baseurl }}"></script>
     <script type="text/javascript" src="{{ "/assets/js/bootstrap.min.js?v=3" | prepend: site.baseurl }}"></script>
     <script type="text/javascript" src="{{ "/assets/js/details-element-polyfill.js" | prepend: site.baseurl }}"></script>
     <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <script type="text/javascript" src="{{ "/assets/js/bootstrap-toc.min.js" | prepend: site.baseurl }}"></script>
     <script type="text/javascript" src="{{ "/assets/js/main.js" | prepend: site.baseurl }}"></script>
 </html>

_layouts/base_slides.html

@@ -37,6 +37,9 @@
     <meta property="og:title" content="Galaxy Training: {{ og_title | truncate: 60}}" />
     <meta property="og:description" content="{{ og_desc | strip_html | truncate: 60}}" />
     <meta property="og:image" content="{{ "/assets/images/GTNLogo1000.png" | prepend: site.baseurl }}" />
+    <script type="application/ld+json">
+      {% include _includes/material.jsonld material=page topic=topic site=site %}
+    </script>
   </head>
   <body>
     <textarea id="source">
@@ -46,6 +49,13 @@
 
 <div class="my-header"><span>
 <a href="{{ site.baseurl }}/topics/{{ topic.name }}" title="Return to topic page" ><i class="fa fa-level-up" aria-hidden="true"></i></a>
+{% if page.type == "introduction" %}
+  {% capture link %}{{ site.github.repository_url }}/edit/{{ site.repository_branch }}/topics/{{ topic.name }}/slides/{{ page.tutorial_name }}.html{% endcapture %}
+{% else %}
+  {% capture link %}{{ site.github.repository_url }}/edit/{{ site.repository_branch }}/topics/{{ topic.name }}/tutorials/{{ page.tutorial_name }}/slides.html{% endcapture %}
+{% endif %}
+<a class="nav-link" href="{{ link }}"><i class="fa fa-pencil" aria-hidden="true"></i></a>
+
 </span></div>
 
 <div class="my-footer"><span>
@@ -61,29 +71,16 @@
 # {{ title }}
 
 {% if topic.requirements or page.requirements %}
+
 ---
 
-  ## Requirements
+## Requirements
 
-  Before diving into this slide deck, we recommend you to have a look at:
+Before diving into this slide deck, we recommend you to have a look at:
+
+{% include snippets/display_extra_training_slides.md extra_trainings=topic.requirements %}
+{% include snippets/display_extra_training_slides.md extra_trainings=page.requirements %}
 
-  {% for requirement in topic.requirements %}
-    {% if requirement.type == "internal" %}
-  - [{{ requirement.title }}]({{ site.baseurl }}/topics{{ requirement.link }})
-    {% elsif requirement.type == "external" %}
-  - [{{ requirement.title }}]({{ requirement.link }})
-    {% endif %}
-  {% endfor %}
-
-  {% if tutorial.requirements %}
-    {% for requirement in tutorial.requirements %}
-      {% if requirement.type == "internal" %}
-  - [{{ requirement.title }}]({{ site.baseurl }}{{ requirement.link }})
-      {% elsif requirement.type == "external" %}
-  - [{{ requirement.title }}]({{ requirement.link }})
-      {% endif %}
-    {% endfor %}
-  {% endif %}
 {% endif %}
 
 ---
@@ -94,7 +91,7 @@
 
 ## Thank you!
 
-This material is the result of a collaborative work. Thanks the [Galaxy Training Network](https://wiki.galaxyproject.org/Teach/GTN) and all the contributors {% if tutorial.contributors %}{% capture contributors %}{% for c in tutorial.contributors %}, {{ contributors[c].name | default: c }}{% endfor %}{% endcapture %} ({{ contributors | remove_first: ', ' }}) {% endif %}!
+This material is the result of a collaborative work. Thanks the [Galaxy Training Network](https://wiki.galaxyproject.org/Teach/GTN) and all the contributors {% if tutorial.contributors %}{% capture contributors %}{% for c in tutorial.contributors %}, [{{ contributors[c].name | default: c }}]({{ site.baseurl }}/hall-of-fame#{{ c }}){% endfor %}{% endcapture %} ({{ contributors | remove_first: ', ' }}) {% endif %}!
 
 {% if page.logo == "GTN" %}
 <img src="{{ site.baseurl }}/{{ site.logo }}" alt="Galaxy Training Network" style="height: 100px;"/>
@@ -103,7 +100,7 @@
 {% endif %}
 
 {% if page.layout == "base_slides" %}
-.footnote[Found a typo? Something is wrong in this tutorial? <br/>Edit it on [GitHub]({{ site.github_repository }}/tree/master{{ page.url }})]
+.footnote[Found a typo? Something is wrong in this tutorial? <br/>Edit it on [GitHub]({{ site.github.repository_url }}/tree/master{{ page.url }})]
 {% endif %}
     </textarea>
     <script src="{{ "/assets/js/remark-latest.min.js" | prepend: site.baseurl }}" type="text/javascript">

_layouts/bibtemplate.html

@@ -0,0 +1,12 @@
+---
+---
+{{reference}}
+    {% if entry.note %}
+    {{ entry.note }}.
+    {% endif %}
+    {% if entry.url %}
+    <a href="{{ entry.url }}">{{ entry.url }}</a>
+    {% endif %}
+    {% if entry.doi %}
+    <a href="https://doi.org/{{ entry.doi }}">{{ entry.doi }}</a>
+    {% endif %}

_layouts/introduction_slides.html

@@ -16,7 +16,7 @@
         {% if material.hands_on == "yes" %}
 - [{{ material.title }}]({{ site.baseurl }}/topics/{{ topic.name }}/tutorials/{{ material.tutorial_name }}/tutorial.html")
         {% elsif material.hands_on == "github" %}
-- [{{ material.title }}]({{ site.github_repository }}/tree/master/topics/{{ topic.name }}/tutorials/{{ material.tutorial_name }}/tutorial.md)
+- [{{ material.title }}]({{ ssite.github.repository_url }}/tree/master/topics/{{ topic.name }}/tutorials/{{ material.tutorial_name }}/tutorial.md)
         {% elsif material.slides == "yes" %}
 - [{{ material.title }}]({{ site.baseurl }}/topics/{{ topic.name }}/tutorials/{{ material.tutorial_name }}/slides.html")
         {% endif %}