width: 100px;
display:inline-block;
}
+
+.arvados-nav-container {
+ top: 70px;
+ height: calc(100% - 70px);
+ overflow: auto;
+ z-index: 2;
+}
+
+.arvados-nav-active {
+ background: rgb(66, 139, 202);
+}
+
+.arvados-nav-active a {
+ color: white;
+}
display: none;
}
}
- .arvados-nav-container {
- top: 70px;
- height: calc(100% - 70px);
- overflow: auto;
- z-index: 2;
- }
- .arvados-nav-active {
- background: rgb(66, 139, 202);
- }
- .arvados-nav-active a {
- color: white;
- }
</style>
</head>
<body>
navbar:
userguide:
- Getting Started:
+ - user/index.html.textile.liquid
- user/getting_started/workbench.html.textile.liquid
- user/getting_started/ssh-access.html.textile.liquid
- user/getting_started/check-environment.html.textile.liquid
- user/reference/api-tokens.html.textile.liquid
- user/reference/sdk-cli.html.textile.liquid
sdk:
+ - Overview:
+ - sdk/index.html.textile.liquid
- Python:
- sdk/python/sdk-python.html.textile.liquid
- sdk/python/python.html.textile.liquid
- sdk/python/crunch-utility-libraries.html.textile.liquid
api:
- Concepts:
+ - api/index.html.textile.liquid
- api/authentication.html.textile.liquid
- api/methods.html.textile.liquid
- api/resources.html.textile.liquid
-<div class="span3">
- <div class="affix-top">
- <div class="well sidebar-nav">
- <ol class="nav nav-list">
- {% for section in site.navbar[page.navsection] %}
- {% for entry in section %}
- <li><span class="nav-header">{{ entry[0] }}</span>
- <ol class="nav nav-list">
+<div class="col-sm-3">
+ <div class="well">
+ <ol class="nav nav-list">
+ {% for section in site.navbar[page.navsection] %}
+ {% for entry in section %}
+ <li><span class="nav-header">{{ entry[0] }}</span>
+ <ol class="nav nav-list">
{% for item in entry[1] %}
- {% assign p = site.pages[item] %}
- <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}>
-
<a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
+ {% assign p = site.pages[item] %}
+ <li {% if p.url == page.url %} class="active activesubnav" {% elsif p.title == page.subnavsection %} class="activesubnav" {% endif %}>
+ <a href="{{ site.baseurl }}{{ p.url }}">{{ p.title }}</a></li>
{% endfor %}
- </ol>
+ </ol>
{% endfor %}
{% endfor %}
- </ol>
- </div>
+ </ol>
</div>
</div>
- <div class="navbar navbar-inverse navbar-fixed-top" style="margin-bottom:0;">
- <div class="navbar-inner">
- <div class="container">
- <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
- <span class="icon-bar"></span>
- <span class="icon-bar"></span>
- <span class="icon-bar"></span>
- </button>
- <a class="brand" href="{{ site.baseurl }}/">Arvados Docs</a>
- <div class="nav-collapse collapse">
- <ul class="nav">
- <li {% if page.navsection == 'userguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/user/">User Guide</a></li>
- <li {% if page.navsection == 'sdk' %} class="active" {% endif %}><a href="{{ site.baseurl }}/sdk/">SDK Reference</a></li>
- <li {% if page.navsection == 'api' %} class="active" {% endif %}><a href="{{ site.baseurl }}/api/">API Reference</a></li>
- <li {% if page.navsection == 'adminguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/admin/">Admin Guide</a></li>
- <li {% if page.navsection == 'installguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/install/">Install Guide</a></li>
- <li><a></a></li>
- <li><a href="https://arvados.org/">arvados.org »</a></li>
- </ul>
- </div><!--/.nav-collapse -->
- </div>
- </div>
+<div class="navbar navbar-default navbar-fixed-top">
+ <div class="container-fluid">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target="#bs-navbar-collapse">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="{{ site.baseurl }}/">Arvados Docs</a>
</div>
+ <div class="collapse navbar-collapse" id="bs-navbar-collapse">
+ <ul class="nav navbar-nav">
+ <li {% if page.navsection == 'userguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/user/">User Guide</a></li>
+ <li {% if page.navsection == 'sdk' %} class="active" {% endif %}><a href="{{ site.baseurl }}/sdk/">SDK Reference</a></li>
+ <li {% if page.navsection == 'api' %} class="active" {% endif %}><a href="{{ site.baseurl }}/api/">API Reference</a></li>
+ <li {% if page.navsection == 'adminguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/admin/">Admin Guide</a></li>
+ <li {% if page.navsection == 'installguide' %} class="active" {% endif %}><a href="{{ site.baseurl }}/install/">Install Guide</a></li>
+ <li><a href="https://arvados.org/" style="padding-left: 2em">arvados.org »</a></li>
+ </ul>
+ </div>
+ </div>
+</div>
<link rel="icon" href="{{ site.baseurl }}/images/favicon.ico" type="image/x-icon">
<link rel="shortcut icon" href="{{ site.baseurl }}/images/favicon.ico" type="image/x-icon">
<link href="{{ site.baseurl }}/css/bootstrap.css" rel="stylesheet">
+ <link href="{{ site.baseurl }}/css/nav-list.css" rel="stylesheet">
+ <link href="{{ site.baseurl }}/css/badges.css" rel="stylesheet">
<style>
html {
height:100%;
}
body {
- padding-top: 41px;
+ padding-top: 61px;
height: 90%; /* If calc() is not supported */
height: calc(100% - 46px); /* Sets the body full height minus the padding for the menu bar */
}
- div.frontpagehero {
- background: #fff;
- height: 270px;
- background-image: url('images/doc-bg.jpg');
- background-repeat: no-repeat;
- color: #fff;
- margin-top:0;
- margin-left:0;
- z-index: -1000;
- opacity: 0.8;
- }
@media (max-width: 979px) {
div.frontpagehero {
margin-left: -20px;
color: #d14;
}
:target {
- padding-top: 41px;
- margin-top: -41px;
+ padding-top: 61px;
+ margin-top: -61px;
}
</style>
<link href="{{ site.baseurl }}/css/bootstrap-responsive.min.css" rel="stylesheet">
{{ content }}
{% else %}
- <div style="height:19px;"></div>
-
<div class="container-fluid">
- <div class="row-fluid">
+ <div class="row">
{% include 'navbar_left' %}
- <div class="span9"><div style="padding-left: 2em;">
+ <div class="col-sm-9">
{{ content }}
- </div></div>
+ </div>
</div>
<div style="height: 2em"></div>
--- /dev/null
+/* Colors
+ * Contextual variations of badges
+ * Bootstrap 3.0 removed contexts for badges, we re-introduce them, based on what is done for labels
+ */
+
+.badge.badge-error {
+ background-color: #b94a48;
+}
+
+.badge.badge-warning {
+ background-color: #f89406;
+}
+
+.badge.badge-success {
+ background-color: #468847;
+}
+
+.badge.badge-info {
+ background-color: #3a87ad;
+}
+
+.badge.badge-inverse {
+ background-color: #333333;
+}
+
+.badge.badge-alert {
+ background: red;
+}
--- /dev/null
+// NAV LIST
+// --------
+
+.nav-list {
+ padding-left: 15px;
+ padding-right: 15px;
+ margin-bottom: 0;
+}
+.nav-list > li > a,
+.nav-list .nav-header {
+ margin-left: -15px;
+ margin-right: -15px;
+ text-shadow: 0 1px 0 rgba(255,255,255,.5);
+}
+.nav-list > li > a {
+ padding: 3px 15px;
+}
+.nav-list > .active > a,
+.nav-list > .active > a:hover,
+.nav-list > .active > a:focus {
+ color: white;
+ text-shadow: 0 -1px 0 rgba(0,0,0,.2);
+ background-color: rgb(66, 139, 202);
+}
title: Arvados | Documentation
...
-<div class="frontpagehero">
- <div style="padding:100px 50px; margin-left:0px; margin-top:0px">
- <p style="font-size: 60px; font-family: Garland, serif;">AR‌<span style="margin-left:-0.07em;margin-right:-0.155em;">V</span>‌ADOS</p>
- <p style="line-height: 1.2em; font-size: 28px; margin-top: 1em;">manuals, guides, and references</p>
+<div class="jumbotron">
+ <div class="container">
+ <div class="row">
+ <div class="col-sm-6">
+ <h1>ARVADOS</h1>
+ <p>manuals, guides, and references</p>
+ </div>
+ <div class="col-sm-6">
+ <img src="images/dax.png" style="max-height: 10em"></img>
+ </div>
+ </div>
</div>
</div>
-<div style="height: 2em;"></div>
-<div style="display: table-row">
- <div style="width: 50px; display: table-cell;">
- </div>
- <div style="width: 300px; display: table-cell;">
- <p>This site contains documentation for the <a href="https://arvados.org/">Arvados platform</a>. The documentation is being developed as part of the open source project. It is a work in progress that has just gotten started. You can get involved by <a href="https://arvados.org/projects/arvados/wiki/Documentation">joining the documentation effort</a>.
- </div>
- <div style="width: 50px; display: table-cell;">
-
- </div>
- <div style="width: 50px; display: table-cell; border-left:1px solid #bbb;">
-
- </div>
- <div style="margin-left: 0px; width: auto; display: table-cell;">
- <div>
+<div class="container-fluid">
+ <div class="row">
+ <div class="col-sm-5">
+ <p>This site contains documentation for the <a href="https://arvados.org/">Arvados platform</a>. The documentation is being developed as part of the open source project. It is a work in progress that has just gotten started. You can get involved by <a href="https://arvados.org/projects/arvados/wiki/Documentation">joining the documentation effort</a>.
+ </div>
+ <div class="col-sm-7" style="border-left: solid; border-width: 1px">
<p>
<a href="{{ site.baseurl }}/user/">User Guide</a> — How to manage data and do analysis with Arvados.
</p>
</p>
<p>
<a href="{{ site.baseurl }}/install/">Install Guide</a> — How to install Arvados on a cloud platform.
- </p>
+ </p>
</div>
</div>
</div>
h3. From the workbench dashboard
-Open the Workbench dashboard (in this guide, this is "https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/ ) and look in upper right corner. If you have no @ssh@ keys registered, there should be a notification asking you to provide your @ssh@ public key. Paste your public key into the text area and click on the check button to submit the key. You are now ready to "log into an Arvados VM":#login.
+If you have no @ssh@ keys registered, there should be a notification asking you to provide your @ssh@ public key. On the Workbench dashboard (in this guide, this is "https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/ ), look for the icon <span class="glyphicon glyphicon-envelope"></span> <span class="badge badge-alert">1</span> in upper right corner. Click on this icon and a dropdown menu should appear with a message asking you to add your public key. Paste your public key into the text area provided and click on the check button to submit the key. You are now ready to "log into an Arvados VM":#login.
h3. Alternate way to add ssh keys
-If you want to add additional @ssh@ keys, use the menu item _Access %(rarr)→% Keys_ to add an authorized ssh key to your account.
+If you want to add additional @ssh@ keys, click on the user icon <span class="glyphicon glyphicon-user"></span> in the upper right corner to access the user settings menu, and click on the menu item _Manage ssh keys_ to add an authorized ssh key to your account.
-Click on the button <span class="btn btn-primary disabled">Add a new authorized key</span>.
+Netx, on _Authorized keys_ page, the click on the button <span class="btn btn-primary disabled">Add a new authorized key</span>
This will reload the page, and should now show a row of information. Under the *public_key* column heading, click on the cell _none_ . This should open up an editing popup as shown in this screenshot:
!{{ site.baseurl }}/images/ssh-adding-public-key.png!
-Paste the public key that you copied to the clipboard in the previous section into the popup text box and click on the check mark to save it. This should refresh the page with the public key that you just added now listed under the *public_key* column. You are now ready to "log into an Arvados VM":#login.
+Paste the public key from the previous section into the popup text box and click on the check mark to save it. This should refresh the page with the public key that you just added now listed under the *public_key* column. You are now ready to "log into an Arvados VM":#login.
h1(#login). Using ssh to log into an Arvados VM
This user guide introduces how to use the major components of Arvados. These are:
-* Keep: Content-addressable cluster file system designed for robust storage of very large files, such as whole genome sequences
+* Keep: Content-addressable cluster file system designed for robust storage of very large files, such as whole genome sequences running in the hundreds of gigabytes
* Crunch: Cluster compute engine designed for genomic analysis, e.g. alignment, variant calls
* Metadata Database: Information about the genomic data stored in Keep, such as genomic traits, human subjects
* Workbench: Web interface to Arvados components
# Using the unix command line shell @bash@
# Viewing and editing files using a unix text editor such as @vi@, @emacs@, or @nano@
# Programming in @python@
-
-It will also be helpful (but not essential) if you are familiar with revision control using @git@.
+# Revision control using @git@
The examples in this guide uses the public Arvados instance located at "https://workbench.{{ site.arvados_api_host }}/":https://workbench.{{ site.arvados_api_host }}/ . You must have an account in order to use this service. If you would like to request an account, please send an email to "arvados@curoverse.com":mailto:arvados@curoverse.com .
projects / arvados.git / commitdiff
