Skip to content

Commit fd0fb89

Browse files
R-Wright-1R-Wright-1
committed
Update pages and front page
- Updated pages for marker gene and metagenome workflow (currently still empty). - Added Microbiome Helper and Langille lab logo to home page. - Added navigation bar to top of all pages.
1 parent 27df467 commit fd0fb89

49 files changed

Lines changed: 8193 additions & 20 deletions

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

‎.DS_Store‎

0 Bytes
Binary file not shown.

‎Gemfile.lock‎

Lines changed: 428 additions & 0 deletions
Large diffs are not rendered by default.

‎README.md‎

Lines changed: 11 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,12 @@
1-
---
2-
layout: landingpage
3-
title: "Microbiome Helper"
4-
---
1+
This repository has the content for [microbiomehelper.ca](www.microbiomehelper.ca).
52

6-
# Welcome to Microbiome Helper
7-
Resources and tutorials for microbiome data analysis. We are currently still building this website, but in the meantime you can view all of our current analysis workflows on our [Github Wiki](https://github.com/LangilleLab/microbiome_helper/wiki/Home-%E2%80%90-Microbiome-Helper-2).
3+
The site is built using [Jekyll](https://jekyllrb.com/docs/) with the [Chulapa](https://dieghernan.github.io/chulapa/docs) skin (there is information on the available theme options in both of these).
4+
5+
To make changes (including new pages), there seem to be several ways, but I recommend several steps:
6+
1. Clone the repository onto your laptop.
7+
2. Follow the directions to install Jekyll on your OS (e.g. [here](https://jekyllrb.com/docs/installation/macos/) for Mac, which meant installing `homebrew`, `chruby`, `ruby-install` and `jekyll`)
8+
3. Change to the directory that your repository is in and run: `bundle install` and `bundle update github-pages`
9+
4. Make any changes that you want to make!
10+
5. Check them using: `bundle exec jekyll serve`
11+
6. When you are ready, build the site using: `bundle exec jekyll build`
12+
7. And push the changes to Github

‎_config.yml‎

Lines changed: 20 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -9,11 +9,27 @@ theme: null
99
# Navigation & Style
1010
chulapa-skin:
1111
skin: "solar"
12-
13-
navbar:
14-
menu: "navigation"
12+
13+
kramdown:
14+
syntax_highlighter_opts:
15+
theme: solarized-light
1516

1617
# Plugins
1718
plugins:
1819
- jekyll-remote-theme
19-
- jekyll-include-cache
20+
- jekyll-include-cache
21+
22+
navbar:
23+
style: classic
24+
expand: md
25+
nav:
26+
- title: "Home"
27+
url: /
28+
- title: Marker gene
29+
url: /docs/marker-gene/
30+
- title: Metagenome first steps
31+
url: /docs/metagenome-initial/
32+
- title: Metagenomic taxonomic annotation
33+
url: /docs/metagenome-taxonomy/
34+
- title: Metagenomic functional annotation
35+
url: /docs/metagenome-function/

‎_data/.DS_Store‎

6 KB
Binary file not shown.

‎_data/navigation.yml‎

Lines changed: 0 additions & 8 deletions
This file was deleted.

‎_site/README.md‎

Lines changed: 38 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,38 @@
1+
This repository has the content for [microbiomehelper.ca](www.microbiomehelper.ca).
2+
3+
The site is built using [Jekyll](https://jekyllrb.com/docs/) with the [Chulapa](https://dieghernan.github.io/chulapa/docs) skin (there is information on the available theme options in both of these).
4+
5+
To make changes (including new pages), there seem to be several ways, but I recommend several steps:
6+
1. Clone the repository onto your laptop.
7+
2. Follow the directions to install Jekyll on your OS (e.g. [here](https://jekyllrb.com/docs/installation/macos/) for Mac, which meant installing `homebrew`, `chruby`, `ruby-install` and `jekyll`)
8+
3. Change to the directory that your repository is in and run: `bundle install` and `bundle update github-pages`
9+
4. Make any changes that you want to make!
10+
5. Check them using: `bundle exec jekyll serve`
11+
6. Confirm them using:
12+
13+
14+
15+
16+
17+
This repository contains the content for the dalmug.org website.
18+
19+
To add a blog post you need to simply create a new file within the /_posts/ directory and it has to be named YEAR-MM-DD-Short-description.md. For example 2017-10-27-Comparative-Metagenomics-of-Blastocystis.md. The description doesn't need to be the post title - that will be specified at the top of file. This should be the date that you post the blog post and not the date the journal club was held. You should also write the title in the below section and make sure that the file ends with the ".md" extension. Also, note that italics, bold, and other formatting settings will not be carried over if you copy the text from elsewhere (but you can do that formatting in markdown as well!).
20+
21+
Once you make the new .md file you need to place this at the very top of the file (including the --- part):
22+
23+
---
24+
published: true
25+
title: INSERT_TEXT_HERE
26+
post_snippet: INSERT_TEXT_HERE
27+
---
28+
For an example of how this would look like for an example post, see here.
29+
30+
Note that you can replace published:true with published:false if you want to simply save it as a draft and wait to publish it later.
31+
32+
The text following post_snippet is the preview of the post that will be shown on the Blog page under the post title.
33+
34+
Note that if you do not specify a title it will be the "Name-of-Post" part of the post file-name. It is better to specify the title yourself so that you can indicate which words should be capitalized.
35+
36+
Formatting is done using Markdown. This Markdown Cheatsheet might come in handy.
37+
38+
Lastly, instead of editing directly on github, you can use http://prose.io which provides a nicer web-based user interface for editing.

‎_site/assets/css/custom.css‎

Whitespace-only changes.

‎_site/assets/css/highlighter.css‎

Lines changed: 212 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,212 @@
1+
.highlight table td { padding: 5px; }
2+
3+
.highlight table pre { margin: 0; }
4+
5+
.highlight .hll { background-color: #ffffcc; }
6+
7+
.highlight pre { background: #f8f8f8; }
8+
9+
.highlight .c { color: #3D7B7B; font-style: italic; }
10+
11+
/* Comment */
12+
.highlight .err { border: 1px solid #F00; }
13+
14+
/* Error */
15+
.highlight .k { color: #008000; font-weight: bold; }
16+
17+
/* Keyword */
18+
.highlight .o { color: #666; }
19+
20+
/* Operator */
21+
.highlight .ch { color: #3D7B7B; font-style: italic; }
22+
23+
/* Comment.Hashbang */
24+
.highlight .cm { color: #3D7B7B; font-style: italic; }
25+
26+
/* Comment.Multiline */
27+
.highlight .cp { color: #9C6500; }
28+
29+
/* Comment.Preproc */
30+
.highlight .cpf { color: #3D7B7B; font-style: italic; }
31+
32+
/* Comment.PreprocFile */
33+
.highlight .c1 { color: #3D7B7B; font-style: italic; }
34+
35+
/* Comment.Single */
36+
.highlight .cs { color: #3D7B7B; font-style: italic; }
37+
38+
/* Comment.Special */
39+
.highlight .gd { color: #A00000; }
40+
41+
/* Generic.Deleted */
42+
.highlight .ge { font-style: italic; }
43+
44+
/* Generic.Emph */
45+
.highlight .ges { font-weight: bold; font-style: italic; }
46+
47+
/* Generic.EmphStrong */
48+
.highlight .gr { color: #E40000; }
49+
50+
/* Generic.Error */
51+
.highlight .gh { color: #000080; font-weight: bold; }
52+
53+
/* Generic.Heading */
54+
.highlight .gi { color: #008400; }
55+
56+
/* Generic.Inserted */
57+
.highlight .go { color: #717171; }
58+
59+
/* Generic.Output */
60+
.highlight .gp { color: #000080; font-weight: bold; }
61+
62+
/* Generic.Prompt */
63+
.highlight .gs { font-weight: bold; }
64+
65+
/* Generic.Strong */
66+
.highlight .gu { color: #800080; font-weight: bold; }
67+
68+
/* Generic.Subheading */
69+
.highlight .gt { color: #04D; }
70+
71+
/* Generic.Traceback */
72+
.highlight .kc { color: #008000; font-weight: bold; }
73+
74+
/* Keyword.Constant */
75+
.highlight .kd { color: #008000; font-weight: bold; }
76+
77+
/* Keyword.Declaration */
78+
.highlight .kn { color: #008000; font-weight: bold; }
79+
80+
/* Keyword.Namespace */
81+
.highlight .kp { color: #008000; }
82+
83+
/* Keyword.Pseudo */
84+
.highlight .kr { color: #008000; font-weight: bold; }
85+
86+
/* Keyword.Reserved */
87+
.highlight .kt { color: #B00040; }
88+
89+
/* Keyword.Type */
90+
.highlight .m { color: #666; }
91+
92+
/* Literal.Number */
93+
.highlight .s { color: #BA2121; }
94+
95+
/* Literal.String */
96+
.highlight .na { color: #687822; }
97+
98+
/* Name.Attribute */
99+
.highlight .nb { color: #008000; }
100+
101+
/* Name.Builtin */
102+
.highlight .nc { color: #00F; font-weight: bold; }
103+
104+
/* Name.Class */
105+
.highlight .no { color: #800; }
106+
107+
/* Name.Constant */
108+
.highlight .nd { color: #A2F; }
109+
110+
/* Name.Decorator */
111+
.highlight .ni { color: #717171; font-weight: bold; }
112+
113+
/* Name.Entity */
114+
.highlight .ne { color: #CB3F38; font-weight: bold; }
115+
116+
/* Name.Exception */
117+
.highlight .nf { color: #00F; }
118+
119+
/* Name.Function */
120+
.highlight .nl { color: #767600; }
121+
122+
/* Name.Label */
123+
.highlight .nn { color: #00F; font-weight: bold; }
124+
125+
/* Name.Namespace */
126+
.highlight .nt { color: #008000; font-weight: bold; }
127+
128+
/* Name.Tag */
129+
.highlight .nv { color: #19177C; }
130+
131+
/* Name.Variable */
132+
.highlight .ow { color: #A2F; font-weight: bold; }
133+
134+
/* Operator.Word */
135+
.highlight .w { color: #BBB; }
136+
137+
/* Text.Whitespace */
138+
.highlight .mb { color: #666; }
139+
140+
/* Literal.Number.Bin */
141+
.highlight .mf { color: #666; }
142+
143+
/* Literal.Number.Float */
144+
.highlight .mh { color: #666; }
145+
146+
/* Literal.Number.Hex */
147+
.highlight .mi { color: #666; }
148+
149+
/* Literal.Number.Integer */
150+
.highlight .mo { color: #666; }
151+
152+
/* Literal.Number.Oct */
153+
.highlight .sa { color: #BA2121; }
154+
155+
/* Literal.String.Affix */
156+
.highlight .sb { color: #BA2121; }
157+
158+
/* Literal.String.Backtick */
159+
.highlight .sc { color: #BA2121; }
160+
161+
/* Literal.String.Char */
162+
.highlight .dl { color: #BA2121; }
163+
164+
/* Literal.String.Delimiter */
165+
.highlight .sd { color: #BA2121; font-style: italic; }
166+
167+
/* Literal.String.Doc */
168+
.highlight .s2 { color: #BA2121; }
169+
170+
/* Literal.String.Double */
171+
.highlight .se { color: #AA5D1F; font-weight: bold; }
172+
173+
/* Literal.String.Escape */
174+
.highlight .sh { color: #BA2121; }
175+
176+
/* Literal.String.Heredoc */
177+
.highlight .si { color: #A45A77; font-weight: bold; }
178+
179+
/* Literal.String.Interpol */
180+
.highlight .sx { color: #008000; }
181+
182+
/* Literal.String.Other */
183+
.highlight .sr { color: #A45A77; }
184+
185+
/* Literal.String.Regex */
186+
.highlight .s1 { color: #BA2121; }
187+
188+
/* Literal.String.Single */
189+
.highlight .ss { color: #19177C; }
190+
191+
/* Literal.String.Symbol */
192+
.highlight .bp { color: #008000; }
193+
194+
/* Name.Builtin.Pseudo */
195+
.highlight .fm { color: #00F; }
196+
197+
/* Name.Function.Magic */
198+
.highlight .vc { color: #19177C; }
199+
200+
/* Name.Variable.Class */
201+
.highlight .vg { color: #19177C; }
202+
203+
/* Name.Variable.Global */
204+
.highlight .vi { color: #19177C; }
205+
206+
/* Name.Variable.Instance */
207+
.highlight .vm { color: #19177C; }
208+
209+
/* Name.Variable.Magic */
210+
.highlight .il { color: #666; }
211+
212+
/* Literal.Number.Integer.Long */

0 commit comments

Comments
 (0)