diff --git a/.vscode/settings.json b/.vscode/settings.json index 23920ad4f..4c0d42de5 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -6,4 +6,4 @@ "source.organizeImports": true } }, -} \ No newline at end of file +} diff --git a/_data/topnav.yml b/_data/topnav.yml index 55de76132..161e82c95 100644 --- a/_data/topnav.yml +++ b/_data/topnav.yml @@ -9,4 +9,22 @@ subitems: url: /training - title: About url: /about - +#Community specific links: +- title: Microbiome + subitems: + - title: Tools + url: /microgalaxy_tools + - title: Workflows + url: /microgalaxy_workflows + - title: Tutorials + url: /microgalaxy_tutorials +#Community specific links are added manually when a lab is created to ensure communities are ready to display them +#To add a community specific tab, copy/paste the template below and replace with you community name and generate a PR +#- title: +# subitems: +# - title: Tools +# url: /_tools +# - title: Workflows +# url: /_workflows +# - title: Tutorials +# url: /_tutorials \ No newline at end of file diff --git a/_includes/communities/microgalaxy/tools.html b/_includes/communities/microgalaxy/tools.html new file mode 100644 index 000000000..b123017f8 --- /dev/null +++ b/_includes/communities/microgalaxy/tools.html @@ -0,0 +1,108 @@ +{%- if include.tag %} +{%- assign tools = site.data.communities.microgalaxy.curated_tools | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.communities.microgalaxy.curated_tools | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + + + + + + + + + + + + {%- for tool in tools %} + + + + + + + + + + + + + + + + {%- endfor %} + +
Suite IDSuite versionDate of first commit of the suiteTool IDsDescriptionEDAM topic(s)EDAM operation(s)Suite runs on main serversbio.tools (if available)Conda idbiiiStatusAvailability across Galaxies
+
+ {% if tool.["Suite ID"] != "" %} + {{ tool.["Suite ID"] }} + {% else %} + {{ tool.["Suite ID"] }} + {% endif %} +
+ 		{{tool.["Suite version"]}}{{tool.["Date of first commit of the suite"]}} + {% if tool.["Tool IDs"] %} {%- for id in tool.["Tool IDs"] %} + + {{id}} + + {%- endfor %} {%- endif %} + {{tool.Description}} + {% if tool.["EDAM topics"] %} {%- for topic in tool.["EDAM topics"] %} + + {{topic}} + + {%- endfor %} {%- endif %} + + {% if tool.["EDAM operations"] %} {%- for operation in tool.["EDAM operations"] %} + + {{operation}} + + {%- endfor %} {%- endif %} + {{tool.["Suite runs on main servers"]}} +
+ {% if tool.["bio.tool ID"] != "null" %} + {{ tool.["bio.tool ID"] }} + {% else %} + "" + {% endif %} +
+ 		+
+ {% if tool.["Suite conda package"] != "null" %} + + {{ tool.["Suite conda package"] }} + + {% endif %} +
+ 		+
+ {% if tool.["biii ID"] != "null" %} + + {{ tool.["biii ID"] }} + + {% endif %} +
+ 		{{tool.["Suite version status"]}} +
+ {% if tool.availability %} {%- for instance in tool.availability %} + + {{instance}} + + {%- endfor %} {%- endif %} +
+
+
+{%- endunless %} +
\ No newline at end of file diff --git a/_includes/communities/microgalaxy/tutorials.html b/_includes/communities/microgalaxy/tutorials.html new file mode 100644 index 000000000..8f806ce79 --- /dev/null +++ b/_includes/communities/microgalaxy/tutorials.html @@ -0,0 +1,60 @@ +{%- if include.tag %} +{%- assign tools = site.data.communities.microgalaxy.tutorials | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.communities.microgalaxy.tutorials | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + + + + + {%- for tool in tools %} + + + + + + + + + {%- endfor %} + +
Title (+link)GTN topic nameLast updatedEDAM topic(s)EDAM operation(s)Resources available
+
+ {% if tool.title != "" %} + {{ tool.title }} + {% else %} + {{ tool.title }} + {% endif %} +
+ 		{{ tool.topic_name_human }}{{ tool.mod_date }} + {% if tool.edam_topic %} {%- for topic in tool.edam_topic %} + + {{topic}} + + {%- endfor %} {%- endif %} + + {% if tool.edam_operation %} {%- for operation in tool.edam_operation %} + + {{operation}} + + {%- endfor %} {%- endif %} + + {% if tool.slides %}Slides{%- endif %} + {% if tool.video %}Video{%- endif %} + {% if tool.hands_on %}Hands-on{%- endif %} +
+
+{%- endunless %} +
\ No newline at end of file diff --git a/_includes/communities/microgalaxy/workflows.html b/_includes/communities/microgalaxy/workflows.html new file mode 100644 index 000000000..adf4cdfd2 --- /dev/null +++ b/_includes/communities/microgalaxy/workflows.html @@ -0,0 +1,76 @@ +{%- if include.tag %} +{%- assign tools = site.data.communities.microgalaxy.curated_workflows | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- else %} +{%- assign tools = site.data.communities.microgalaxy.curated_workflows | add_related_pages | sort_natural: "name" %} +{%- endif %} +{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} +{%- unless tools.size == 0 or tools == nil %} +Skip tool table +
+ + + + + + + + + + + + + + + + {%- for tool in tools %} + + + + + + + + + + + + {%- endfor %} + +
Workflow name (+link)Creation timeLast updatedLicenseEDAM topic(s)EDAM operation(s)Tag(s)DOISource
+
+ {% if tool.name != "" %} + {{ tool.name }} + {% else %} + {{ tool.name }} + {% endif %} +
+ 		{{ tool.create_time }}{{ tool.update_time }}{{ tool.license }} + {% if tool.edam_topic %} {%- for topic in tool.edam_topic %} + + {{topic}} + + {%- endfor %} {%- endif %} + + {% if tool.edam_operation %} {%- for operation in tool.edam_operation %} + + {{operation}} + + {%- endfor %} {%- endif %} + + {% if tool.tags %} {%- for tag in tool.tags %} + + {{tag}} + + {%- endfor %} {%- endif %} + +
+ {% if tool.doi != "null" %} + DOI + {% else %} + "" + {% endif %} +
+ 		{{ tool.source }}
+
+{%- endunless %} +
\ No newline at end of file diff --git a/pages/microgalaxy_tools.md b/pages/microgalaxy_tools.md new file mode 100644 index 000000000..ba011cbd6 --- /dev/null +++ b/pages/microgalaxy_tools.md @@ -0,0 +1,11 @@ +--- +title: Tools +description: An interactive list of Galaxy tools created by the Galaxy CoDex for a specific community. +datatable: true +sidebar: false +toc: false +--- + +
+{% include communities/microgalaxy/tools.html %} +
\ No newline at end of file diff --git a/pages/microgalaxy_tutorials.md b/pages/microgalaxy_tutorials.md new file mode 100644 index 000000000..a3049ffc0 --- /dev/null +++ b/pages/microgalaxy_tutorials.md @@ -0,0 +1,11 @@ +--- +title: Tutorials +description: An interactive list of Galaxy tutorials created by the Galaxy CoDex for a specific community. +datatable: true +sidebar: false +toc: false +--- + +
+{% include communities/microgalaxy/tutorials.html %} +
diff --git a/pages/microgalaxy_workflows.md b/pages/microgalaxy_workflows.md new file mode 100644 index 000000000..410997246 --- /dev/null +++ b/pages/microgalaxy_workflows.md @@ -0,0 +1,11 @@ +--- +title: Workflows +description: An interactive list of Galaxy workflows created by the Galaxy CoDex for a specific community. +datatable: true +sidebar: false +toc: false +--- + +
+{% include communities/microgalaxy/workflows.html %} +
diff --git a/sources/bin/get_community_tools.sh b/sources/bin/get_community_tools.sh index 36707a034..83db26a1b 100755 --- a/sources/bin/get_community_tools.sh +++ b/sources/bin/get_community_tools.sh @@ -35,6 +35,13 @@ for com_data_fp in communities/* ; do if [[ -e "communities/$community/resources/curated_tools.yml" ]]; then mkdir -p _data/communities/$community/ ln -sf ../../../communities/$community/resources/curated_tools.yml _data/communities/$community/curated_tools.yml + #For pages - Can't copy from template, need to copy from existing md file + cp pages/microgalaxy_tools.md pages/${community}_tools.md + sed -i -e "s/microgalaxy/${community}/g" pages/${community}_tools.md + #For _includes - To keep same process as above, copying from existing file + mkdir -p _includes/communities/$community/ + cp _includes/communities/microgalaxy/tools.html _includes/communities/$community/tools.html + sed -i -e "s/microgalaxy/${community}/g" _includes/communities/$community/tools.html fi; if [[ -e "communities/$community/resources/curated_tools.tsv" ]]; then diff --git a/sources/bin/get_community_tutorials.sh b/sources/bin/get_community_tutorials.sh index 438ce86a8..a6d997a3d 100644 --- a/sources/bin/get_community_tutorials.sh +++ b/sources/bin/get_community_tutorials.sh @@ -21,6 +21,13 @@ for com_data_fp in communities/* ; do if [[ -f "communities/$community/resources/tutorials.yml" ]]; then mkdir -p _data/communities/$community/ ln -sf ../../../communities/$community/resources/tutorials.yml _data/communities/$community/tutorials.yml + #For pages - Can't copy from template, need to copy from existing md file + cp pages/microgalaxy_tutorials.md pages/${community}_tutorials.md + sed -i -e "s/microgalaxy/${community}/g" pages/${community}_tutorials.md + #For _includes - To keep same process as above, copying from existing file + mkdir -p _includes/communities/$community/ + cp _includes/communities/microgalaxy/tutorials.html _includes/communities/$community/tutorials.html + sed -i -e "s/microgalaxy/${community}/g" _includes/communities/$community/tutorials.html fi; if [[ -e "communities/$community/resources/tutorials.tsv" ]]; then diff --git a/sources/bin/get_community_workflows.sh b/sources/bin/get_community_workflows.sh index 2e153f7c6..d2265eaf2 100644 --- a/sources/bin/get_community_workflows.sh +++ b/sources/bin/get_community_workflows.sh @@ -31,6 +31,13 @@ for com_data_fp in communities/* ; do if [[ -f "communities/$community/metadata/curated_workflows.yml" ]]; then mkdir -p _data/communities/$community/ ln -sf ../../../communities/$community/resources/curated_workflows.yml _data/communities/$community/curated_workflows.yml + #For pages - Can't copy from template, need to copy from existing md file + cp pages/microgalaxy_workflows.md pages/${community}_workflows.md + sed -i -e "s/microgalaxy/${community}/g" pages/${community}_workflows.md + #For _includes - To keep same process as above, copying from existing file + mkdir -p _includes/communities/$community/ + cp _includes/communities/microgalaxy/workflows.html _includes/communities/$community/workflows.html + sed -i -e "s/microgalaxy/${community}/g" _includes/communities/$community/workflows.html fi; if [[ -e "communities/$community/resources/curated_workflows.tsv" ]]; then