-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html
212 lines (189 loc) · 10 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="description" content="Instructions for OLC Redmine Usage" /><link rel="canonical" href="https://olc-bioinformatics.github.io/redmine-docs/" />
<link rel="shortcut icon" href="img/favicon.ico" />
<title>OLC Redmine Automator</title>
<link rel="stylesheet" href="css/theme.css" />
<link rel="stylesheet" href="css/theme_extra.css" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.5.0/styles/github.min.css" />
<script>
// Current page data
var mkdocs_page_name = "Home";
var mkdocs_page_input_path = "index.md";
var mkdocs_page_url = "/redmine-docs/";
</script>
<script src="js/jquery-3.6.0.min.js" defer></script>
<!--[if lt IE 9]>
<script src="js/html5shiv.min.js"></script>
<![endif]-->
<script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/10.5.0/highlight.min.js"></script>
<script>hljs.initHighlightingOnLoad();</script>
</head>
<body class="wy-body-for-nav" role="document">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side stickynav">
<div class="wy-side-scroll">
<div class="wy-side-nav-search">
<a href="." class="icon icon-home"> OLC Redmine Automator
</a><div role="search">
<form id ="rtd-search-form" class="wy-form" action="./search.html" method="get">
<input type="text" name="q" placeholder="Search docs" title="Type search term here" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<ul class="current">
<li class="toctree-l1 current"><a class="reference internal current" href=".">Home</a>
<ul class="current">
</ul>
</li>
</ul>
<ul>
<li class="toctree-l1"><a class="reference internal" href="getting_started/">Getting Started</a>
</li>
</ul>
<p class="caption"><span class="caption-text">Data</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="data/external_retrieve/">External Retrieve</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="data/report_retrieve/">Report Retrieve</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="data/sra_upload/">SRA Upload</a>
</li>
</ul>
<p class="caption"><span class="caption-text">Analysis</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="analysis/amrsummary/">AMRsummary</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/autoclark/">AutoCLARK</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/confindr/">ConFindr</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/cowsnphr/">COWSNPhR</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/closerelatives/">CloseRelatives</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/eCGF/">eCGF</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/ectyper/">ECTyper</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/diversitree/">DiversiTree</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/geneseekr/">GeneSeekr</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/intimintyper/">IntiminTyper</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/mobsuite/">MobSuite</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/neartree/">NearTree</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/plasmidborneidentity/">PlasmidBorneIdentity</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/pointfinder/">PointFinder</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/primerfinder/">PrimerFinder</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/prokka/">Prokka</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/psortb/">PSORTb</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/resfinder/">ResFinder</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/roary/">Roary</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/sipprverse/">sipprverse</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/snvphyl/">SNVPhyl</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/staramr/">staramr</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/strainmash/">StrainMash</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="analysis/wgsassembly/">WGS Assembly</a>
</li>
</ul>
<p class="caption"><span class="caption-text">Internal Use</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="internal_only/merge/">Merge</a>
</li>
</ul>
<ul>
<li class="toctree-l1"><a class="reference internal" href="troubleshooting/">Troubleshooting</a>
</li>
</ul>
<p class="caption"><span class="caption-text">Tutorials</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="tutorials/create_environment/">Create Environment</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/create_pages/">Create Pages</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/edit_pages/">Edit Pages</a>
</li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/publish_changes/">Publish Changes</a>
</li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="Mobile navigation menu">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href=".">OLC Redmine Automator</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content"><div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="." class="icon icon-home" alt="Docs"></a> »</li><li>Home</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div class="section" itemprop="articleBody">
<h1 id="olc-redmine-automator">OLC Redmine Automator</h1>
<p>To facilitate the sharing of the CFIA's genomic data and tools to analyze this data, we make use of the Redmine
platform. Our instance of Redmine can be found <a href="https://redmine.biodiversity.agr.gc.ca">here</a> (note that you must be on
the CFIA network in order to access Redmine).</p>
<p>If you have not yet gotten started with Redmine or want to know how the Redmine automator works and what it can do,
take a look at our <a href="getting_started/">Getting Started</a> page for instructions on how to start using Redmine and a
brief overview of what Redmine can do.</p>
<p>For any issues or general help with Redmine, see the <a href="troubleshooting/">Troubleshooting</a> page.</p>
</div>
</div><footer>
<div class="rst-footer-buttons" role="navigation" aria-label="Footer Navigation">
<a href="getting_started/" class="btn btn-neutral float-right" title="Getting Started">Next <span class="icon icon-circle-arrow-right"></span></a>
</div>
<hr/>
<div role="contentinfo">
<!-- Copyright etc -->
</div>
Built with <a href="https://www.mkdocs.org/">MkDocs</a> using a <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<div class="rst-versions" role="note" aria-label="Versions">
<span class="rst-current-version" data-toggle="rst-current-version">
<span><a href="getting_started/" style="color: #fcfcfc">Next »</a></span>
</span>
</div>
<script>var base_url = '.';</script>
<script src="js/theme_extra.js" defer></script>
<script src="js/theme.js" defer></script>
<script src="search/main.js" defer></script>
<script defer>
window.onload = function () {
SphinxRtdTheme.Navigation.enable(true);
};
</script>
</body>
</html>
<!--
MkDocs version : 1.3.0
Build Date UTC : 2022-06-08 17:59:40.803063+00:00
-->