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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,87 +1,133 @@ | ||
| # This is your sidebar TOC. The sidebar code loops through sections here and provides the appropriate formatting. | ||
|
|
||
| entries: | ||
| - title: sidebar | ||
| product: | ||
| version: | ||
|
|
||
| folders: | ||
| - title: | ||
| output: pdf | ||
| type: frontmatter | ||
| folderitems: | ||
| - title: | ||
| url: /titlepage.html | ||
| output: pdf | ||
| type: frontmatter | ||
| - title: | ||
| url: /tocpage.html | ||
| output: pdf | ||
| type: frontmatter | ||
|
|
||
| - title: Overview | ||
| output: web, pdf | ||
| folderitems: | ||
|
|
||
| - title: Getting Started | ||
| url: /index.html | ||
| - title: sidebar | ||
| product: | ||
| version: | ||
|
|
||
| folders: | ||
| - title: | ||
| output: pdf | ||
| type: frontmatter | ||
| folderitems: | ||
| - title: | ||
| url: /titlepage.html | ||
| output: pdf | ||
| type: frontmatter | ||
| - title: | ||
| url: /tocpage.html | ||
| output: pdf | ||
| type: frontmatter | ||
|
|
||
| - title: Overview | ||
| output: web, pdf | ||
| type: homepage | ||
| folderitems: | ||
|
|
||
| - title: Example Workflow | ||
| url: /como_example_workflow.html | ||
| output: web, pdf | ||
| - title: Getting Started | ||
| url: /index.html | ||
| output: web, pdf | ||
| type: homepage | ||
|
|
||
| - title: Flow Charts | ||
| url: /como_flowcharts.html | ||
| output: web, pdf | ||
| - title: Example Workflow | ||
| url: /como_example_workflow.html | ||
| output: web, pdf | ||
|
|
||
| - title: Resources | ||
| url: /como_resources.html | ||
| output: web, pdf | ||
| - title: Flow Charts | ||
| url: /como_flowcharts.html | ||
| output: web, pdf | ||
|
|
||
| - title: Resources | ||
| url: /como_resources.html | ||
| output: web, pdf | ||
|
|
||
| - title: Repository Structure | ||
| url: /como_repository_structure.html | ||
| - title: Docker Installation Method | ||
| output: web, pdf | ||
| folderitems: | ||
| - title: Overview | ||
| url: /como_docker_overview.html | ||
| output: web, pdf | ||
|
|
||
| - title: Arguments | ||
| output: web | ||
| folderitems: | ||
| - title: Installing Docker | ||
| url: /como_docker_installation.html | ||
| output: web, pdf | ||
|
|
||
| - title: Pulling the Container | ||
| url: /como_docker_pull_container.html | ||
| output: web, pdf | ||
|
|
||
| - title: Obtaining a Gurobi License | ||
| url: /como_docker_gurobi_license.html | ||
| output: web, pdf | ||
|
|
||
| - title: Arguments Overview | ||
| url: /como_arguments_overview.html | ||
| - title: Starting the Container | ||
| url: /como_docker_start_container.html | ||
| output: web, pdf | ||
|
|
||
| - title: Conda Installation Method | ||
| output: web, pdf | ||
| folderitems: | ||
| - title: Overview | ||
| url: /como_conda_overview.html | ||
| output: web, pdf | ||
|
|
||
| subfolders: | ||
| - title: Python Arguments | ||
| url: /como_python_arguments.html | ||
| - title: Conda/Mamba Installation | ||
| url: /como_conda_installation.html | ||
| output: web, pdf | ||
| subfolderitems: | ||
|
|
||
| - title: Create Context Specific Model | ||
| url: /como_args_create_context_specific_model.html | ||
| output: web, pdf | ||
| - title: Clone COMO Repository | ||
| url: /como_clone_repository.html | ||
| output: web, pdf | ||
|
|
||
| - title: Disease Analysis | ||
| url: /como_args_disease_analysis.html | ||
| output: web, pdf | ||
| - title: Install Dependencies | ||
| url: /como_install_dependencies.html | ||
| output: web, pdf | ||
|
|
||
| - title: Knockout Simulation | ||
| url: /como_args_knockout_simulation.html | ||
| output: web, pdf | ||
| - title: Obtaining a Gurobi License | ||
| url: /como_conda_gurobi_license.html | ||
| output: web, pdf | ||
|
|
||
| - title: Merge Omics | ||
| url: /como_args_merge_xomics.html | ||
| output: web, pdf | ||
| - title: Start COMO | ||
| url: /como_start_notebook.html | ||
| output: web, pdf | ||
|
|
||
| - title: Proteomics Gen | ||
| url: /como_args_proteomics_gen.html | ||
| output: web, pdf | ||
| - title: API Arguments | ||
| output: web | ||
| folderitems: | ||
|
|
||
| - title: RNA Seq Gen | ||
| url: /como_args_rnaseq_gen.html | ||
| output: web, pdf | ||
| - title: Arguments Overview | ||
| url: /como_arguments_overview.html | ||
| output: web, pdf | ||
|
|
||
| - title: RNA Seq Preprocess | ||
| url: /como_args_rnaseq_preprocess.html | ||
| subfolders: | ||
| - title: Python Arguments | ||
| url: /como_python_arguments.html | ||
| output: web, pdf | ||
| subfolderitems: | ||
|
|
||
| - title: Create Context Specific Model | ||
| url: /como_args_create_context_specific_model.html | ||
| output: web, pdf | ||
|
|
||
| - title: Disease Analysis | ||
| url: /como_args_disease_analysis.html | ||
| output: web, pdf | ||
|
|
||
| - title: Knockout Simulation | ||
| url: /como_args_knockout_simulation.html | ||
| output: web, pdf | ||
|
|
||
| - title: Merge Omics | ||
| url: /como_args_merge_xomics.html | ||
| output: web, pdf | ||
|
|
||
| - title: Proteomics Gen | ||
| url: /como_args_proteomics_gen.html | ||
| output: web, pdf | ||
|
|
||
| - title: RNA Seq Gen | ||
| url: /como_args_rnaseq_gen.html | ||
| output: web, pdf | ||
|
|
||
| - title: RNA Seq Preprocess | ||
| url: /como_args_rnaseq_preprocess.html | ||
| output: web, pdf |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,9 +1,7 @@ | ||
| ## Topnav single links | ||
| ## if you want to list an external url, use external_url instead of url. the theme will apply a different link base. | ||
| topnav: | ||
| - title: Topnav | ||
| items: | ||
| - title: News | ||
| url: /news | ||
| - title: GitHub | ||
| external_url: https://github.com/HelikarLab/COMO | ||
| - title: Topnav | ||
| items: | ||
| - title: GitHub | ||
| external_url: https://github.com/HelikarLab/COMO |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,15 +1,17 @@ | ||
| <li> | ||
| {% if site.feedback_text %} | ||
| {% if site.feedback_text %} | ||
| {% assign feedback_text = site.feedback_text %} | ||
| {% else %} | ||
| {% else %} | ||
| {% assign feedback_text = "Feedback" %} | ||
| {% endif %} | ||
|
|
||
| {% if site.feedback_link %} | ||
| <a class="email" title="Submit feedback" href="{{site.feedback_link}}">{{feedback_text}}</a> | ||
| {% else %} | ||
| <a class="email" title="Submit feedback" href="#" onclick="javascript:window.location='mailto:{{site.feedback_email}}?subject={{site.feedback_subject_line}} feedback&body=I have some feedback about the {{page.title}} page: ' + window.location.href;"><i class="fa fa-envelope-o"></i> {{feedback_text}}</a> | ||
| {% endif %} | ||
| {% endif %} | ||
|
|
||
| {% if site.feedback_link %} | ||
| <a class="email" title="Submit feedback" href="{{site.feedback_link}}" target="_blank">{{feedback_text}}</a> | ||
| {% else %} | ||
| <a class="email" title="Submit feedback" href="#" | ||
| onclick="javascript:window.location='mailto:{{site.feedback_email}}?subject={{site.feedback_subject_line}} feedback&body=I have some feedback about the {{page.title}} page: ' + window.location.href;"><i | ||
| class="fa fa-envelope-o"></i> {{feedback_text}}</a> | ||
| {% endif %} | ||
| </li> | ||
|
|
||
| {% comment %} Copyright 2021 Google LLC {% endcomment %} |
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