mo

src/assets/CSS/custom.css

@@ -1,3 +1,49 @@
+
+.sphinxsidebar .sphinxsidebarwrapper {
+    text-align: center;
+}
+.sphinxsidebarwrapper {
+    padding-top: 200px;
+    position: fixed;
+    width: 200px;
+    top: 20px;
+    bottom: 0;
+    overflow-y: auto; 
+}
+
+
+
+
+.sphinxsidebar .logo {
+    padding-bottom: 20px;
+}
+
 div.body {
-    max-width: 1000px;  /* Adjust this value as needed */
+    min-width: 900px;
+    max-width: 1000px;
+}
+
+.centered {
+    text-align: center;
+}
+
+
+.sphinxsidebar {
+    width: 20%;
+}
+
+.documentwrapper {
+    max-width: 80%;
+    margin-left: auto;
+    margin-right: auto;
+}
+
+.wy-nav-content {
+    max-width: 100%;
+}
+
+div.bodywrapper {
+    margin-top: 0px;
+    margin-left: 20px;
+
 }

src/conf.py

@@ -57,10 +57,43 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 
+def setup(app):
+    app.add_css_file('my_theme.css')
+
 # Create custom css for the webpage
 html_static_path = ["assets/CSS", "assets/images"]
 html_css_files = ["custom.css"]
 
-html_logo = "assets/images/logo.png"
-html_theme_options = {'logo_only': True, 'nosidebar': True}
-html_title = "Welcome Page"
+
+
+html_sidebars = {
+    '**': [
+        # 'about.html',
+        'navigation.html',
+        'relations.html',  # Optionally include this if you want "next" and "previous" links
+        # 'searchbox.html'  # This line is commented out or removed to exclude the search box
+    ]
+}
+
+
+# html_sidebars = {
+#     '**': [
+#         #'custom_sidebar.html',  # Your custom template
+#         'navigation.html',
+#         #'searchbox.html',
+#         # Add other sidebar elements as needed
+#     ]
+# }
+
+
+html_logo = "assets/images/some_logo.png"
+
+html_theme_options = {
+
+    #'logo_only': False, 
+    'nosidebar': False,
+    #'show_relbar_bottom': True,
+    'sidebar_width': '225px',
+    #'sidebar_depth': 2,
+}
+html_title = "RBPBench Website"

src/docs/documentation.md

@@ -0,0 +1,5 @@
+# Documentation
+
+A detailed documentation for RBPBench can be found in the [GitHub repository](https://github.com/michauhl/RBPBench).
+For more details on how to use the RBPBench webserver, please refer to the [webserver tutorial](webserver_tutorial.md), 
+or the help section at the bottom of the [webserver page](https://usegalaxy.eu), which describes the available program modes.

src/docs/faq.md

@@ -0,0 +1,15 @@
+# FAQ
+
+
+**Where can I get the standalone version of RBPBench?**
+
+For the Linux command line version of RBPBench on which the webserver version is based on, 
+please visit the RBPBench [GitHub repository](https://github.com/michauhl/RBPBench).
+There you can also detailed installation instructions, as well as usage examples and 
+a comprehensive documentation.
+
+
+**Where to send bug reports and feature requests?**
+
+You can either open up a new issue in the RBPBench [GitHub repository](https://github.com/michauhl/RBPBench) 
+(especially for requests and command line related bugs), or send bug reports directly on Galaxy.

src/docs/webserver_tutorial.md

@@ -0,0 +1,6 @@
+# Webserver Tutorial
+
+This short tutorial provides a quick overview on how to use the [RBPBench webserver](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/rbpbench/rbpbench/0.8+galaxy0) 
+on Galaxy, including some real data usage examples.
+
+Coming soon ...

src/index.md

@@ -1,36 +1,34 @@
-# RBPBench
+# Welcome to RBPBench!
 
-[RBPBench](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/rbpbench/rbpbench/0.7+galaxy0) is multi-function tool to evaluate CLIP-seq and other genomic region data
-using a comprehensive collection of known RBP binding motifs. RBPBench can be used
-for a variety of purposes, from RBP motif search (database or user-supplied RBPs)
-in genomic regions, over motif co-occurrence analysis, to benchmarking CLIP-seq peak
+RBPBench is multi-function tool to evaluate CLIP-seq and other genomic region data 
+using a comprehensive collection of known RBP binding motifs. RBPBench can be used 
+for a variety of purposes, from RBP motif search (database or user-supplied RBPs) 
+in genomic regions, over motif co-occurrence analysis, to benchmarking CLIP-seq peak 
 caller methods as well as comparisons across cell types and CLIP-seq protocols.
 
-## [RBPBench Webserver on Galaxy](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/rbpbench/rbpbench/0.7+galaxy0)
+```{toctree}
+:hidden:
+:maxdepth: 1
 
-## RBPBench Galaxy Tutorials
+docs/webserver_tutorial.md
+docs/documentation.md
+docs/faq.md
+```
 
-- [Basic Galaxy introduction and RBPBench user interface](docs/tutorial/intro.md)
+[Webserver on Galaxy](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/rbpbench/rbpbench/0.8+galaxy0)
+
+[Webserver Tutorial](docs/webserver_tutorial.md)
+
+[GitHub repository](https://github.com/michauhl/RBPBench)
 
-## RBPBench results
 
 ![RBPBench example visualizations](assets/images/rbpbench_visualization_examples.png)
 <span style="font-size: 90%;">
-**Figure**: Some example visualizations produced by RBPBench.
-**a**: RBP binding motif co-occurrence heat map.
-**b**: What RBP binding motif combinations appear in the data.
-**c**: Motif distances in the data relative to an RBP of interest.
-**d**: To which region types RBPs preferentially bind to.
-**e**: Comparing CLIP-seq peak calling methods.
+**Figure**: Some example visualizations produced by RBPBench. 
+**a**: RBP binding motif co-occurrence heat map. 
+**b**: What RBP binding motif combinations appear in the data. 
+**c**: Motif distances in the data relative to an RBP of interest. 
+**d**: To which region types RBPs preferentially bind to. 
+**e**: Comparing CLIP-seq peak calling methods. 
 **f**: Comparing experimental conditions.
 </span>
-
-## Additional Links
-
-RBPBench [GitHub repository](https://github.com/michauhl/RBPBench)
-
-RBPBench [Bioconda package](https://bioconda.github.io/recipes/rbpbench/README.html)
-
-## RBP motif data
-
-List of [RBPs and number of available motifs per RBP](docs/tutorial/RBPs.md)