--- /dev/null
+{% if run_f %}
+ <ul>
+ RUN FOLDER: <li>{{ run_f.run_folder }}</li>
+ </ul>
+{% else %}
+ <p>Run folder not found.</p>
+{% endif %}
--- /dev/null
+{% extends "base.html" %}
+{% load i18n %}
+
+{% block breadcrumbs %}
+<div class="breadcrumbs">
+ <a href="/admin">{% trans 'Home' %}</a> ›
+ <a href="/admin/experiments">Experiments</a> ›
+ <a href="/admin/experiments/flowcell">flowcell</a> ›
+ <a href="{{ flowcell.get_admin_url }}">{{ flowcell.flowcell_id }}</a>
+</div>
+{% endblock %}
+
+{% block content %}
+{% if warnings %}
+<hr/>
+<p>
+{% for user_admin_url, username in warnings %}
+Warning: User <a href="{{ user_admin_url}}">{{ username }}</a> has no
+email address <br/>
+{% endfor %}
+{% endif %}
+</p>
+{% for to, subject, body, sending in emails %}
+<hr/>
+{% if sending %}<b>Message:</b> {{ sending }}<br/>{% endif %}
+<b>From:</b> {{ from }}<br/>
+<b>To:</b> {{ to }}<br/>
+<b>Subject:</b> {{ subject }}<br/>
+<pre>
+{{ body }}
+</pre>
+{% endfor %}<hr/>
+<form method="get">
+<label for="bcc">BCC {% for m in site_managers %}{{ m }} {% endfor %}</label>
+<input type="checkbox" id="bcc" name="bcc" checked="on"/><br/>
+<input type="hidden" name="send" value="1"/>
+<input type="submit" value="Send Email"/>
+{% endblock %}
\ No newline at end of file
--- /dev/null
+<html><head><title>{{ fc.flowcell_id }} - GA SEQUENCING (SOLEXA) LOG</title>
+<style type="text/css">
+<!--
+TD
+ {
+ color:black;
+ font-size:9pt;
+ font-face:Arial;
+ }
+-->
+</style>
+</head><body>
+{% if fc %}
+<table border="1" cellspacing="1">
+<tr><td colspan=2 nowrap><b>GA SEQUENCING (SOLEXA) LOG</b></td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td>Date Run Started</td><td colspan=2>{{ fc.run_date }}</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td>Cluster station used</td><td colspan=2 nowrap>{{ fc.cluster_station.name }}</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td>GA used</td><td colspan=2 nowrap>{{ fc.sequencer.name }}</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+
+<tr><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td>Flowcell number</td><td colspan=2 nowrap>{{ fc.flowcell_id }}</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td>Number of Tiles per Lane</td><td>100</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td>Number of Cycles</td><td>{{ fc.read_length }}</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td><font point-size="9" face="Arial"><b>SAMPLE INFORMATION</b><font></td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr><td> </td><td>FC#</td><td> </td><td> </td><td> </td><td> </td><td> </td><td colspan=2 nowrap>FC bar code</td></tr>
+
+<tr><td valign=middle nowrap>Lane</td>
+{% for lane in fc.lane_set.all %}
+<td>{{ lane.lane_number }}</td>
+{% endfor %}
+</tr>
+<tr><td valign=middle nowrap>Solexa Library Number</td>
+{% for lane in fc.lane_set.all %}
+<td bgcolor=#CCFFCC>{{ lane.library.id }}</td>
+{% endfor %}
+</tr>
+
+<tr><td valign=middle nowrap>Sample Name</td>
+{% for lane in fc.lane_set.all %}
+<td bgcolor=#CCFFCC>{{ lane.library.library_name }}</td>
+{% endfor %}
+</tr>
+
+<tr><td valign=middle nowrap>Organism</td>
+{% for lane in fc.lane_set.all %}
+<td bgcolor=#CCFFCC>{{ lane.library.library_species.scientific_name }}</td>
+{% endfor %}
+</tr>
+
+<tr><td valign=middle nowrap>Submitter</td>
+{% for lane in fc.lane_set.all %}
+<td bgcolor=#CCFFCC>{{ lane.library.made_for }}</td>
+{% endfor %}
+</tr>
+
+
+<tr><td valign=middle nowrap>First time run?</td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td></tr>
+
+<tr><td valign=middle nowrap>Gel Cut Size (bp)</td>
+{% for lane in fc.lane_set.all %}
+<td bgcolor=#CCFFCC>{{ lane.library.gel_cut_size }}</td>
+{% endfor %}
+</tr>
+
+<tr><td valign=middle nowrap>Template Concentration (ng/ul)</td>
+{% for lane in fc.lane_set.all %}
+<td bgcolor=#CCFFCC>{{ lane.library.undiluted_concentration }}</td>
+{% endfor %}
+</tr>
+
+<tr><td valign=middle nowrap>Run Concentration (pM)</td>
+{% for lane in fc.lane_set.all %}
+<td bgcolor=#CCFFCC>{{ lane.pM }}</td>
+{% endfor %}
+</tr>
+
+</table>
+
+{% else %}
+ <p>Flowcell object missing. Can't create sheet.</p>
+{% endif %}
+
+</body></html
--- /dev/null
+{% extends "base_site.html" %}
+{% load staticfiles %}
+{% load humanize i18n %}
+{% block extrahead %}
+ <!-- App Stuff -->
+ <link type="text/css" rel="stylesheet" href="{% static "css/app.css" %}" />
+ <script type="text/javascript" src="{% static "js/jquery.min.js" %}"></script>
+
+ {% block additional_javascript %}
+ {% endblock %}
+{% endblock %}
+
+{% block content %}
+<div>
+ {% include "experiments/flowcell_header.html" %}
+ <div class="htswdetail" typeof="libns:IlluminaFlowcell" resource="{{flowcell.get_absolute_url}}">
+ <h2>Lanes</h2>
+ <table>
+ <thead>
+ <tr>
+ <td>Lane</td>
+ <td>Library ID</td>
+ <td>Library Name</td>
+ <td>Species</td>
+ <td>Comment</td>
+ </tr>
+ </thead>
+ <tbody>
+ {% for lane in lanes %}
+ <tr>
+ <td rel="libns:has_lane">
+ <a href="{{lane.get_absolute_url}}" typeof="libns:IlluminaLane">
+ <span property="libns:lane_number">{{lane.lane_number}}</span>
+ </a>
+ </td>
+ <td rel="libns:library"
+ about="{{lane.get_absolute_url}}"
+ resource="{{lane.library.get_absolute_url}}">
+ <a typeof="libns:Library" href="{{lane.library.get_absolute_url}}">
+ <span property="libns:library_id"
+ >{{lane.library.id}}</span></a>
+ {% if user.is_staff %}
+ <a href="{{lane.library.get_admin_url}}">
+ <img class="icon_button"
+ src="{% static "admin/img/icon_changelink.gif" %}"/>
+ </a>{% endif %}
+ </td>
+ <td>
+ <a href="{{lane.library.get_absolute_url}}">
+ <span property="libns:name"
+ about="{{lane.library.get_absolute_url}}"
+ >{{lane.library.library_name}}</span>
+ </a>
+ </td>
+ <td about="{{lane.library.get_absolute_url}}" rel="libns:species">
+ <a href="{{lane.library.library_species.get_absolute_url}}"
+ typeof="libns:Species">
+ <span property="libns:species_name">{{ lane.library.library_species.scientific_name }}</span></a>
+ </td>
+ <td about="{{lane.get_absolute_url}}">
+ <span property="libns:comment">{{lane.comment}}</span>
+ </td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ <div class="htsw_flowcell_ivc">
+ {% for run in flowcell.datarun_set.all %}
+ <h2>Run {{ run.runfolder_name }}</h2>
+ {% if run.lane_files %}
+ <table>
+ <thead>
+ <tr>
+ <td>Lane</td>
+ <td>IVC All</td>
+ <td>IVC Call</td>
+ <td>IVC Percent Base</td>
+ <td>IVC Percent Base All</td>
+ <td>IVC Percent Base Called</td>
+ </tr>
+ </thead>
+ <tbody>
+ {% for lane_id, lane_file_set in run.lane_files.items %}
+ {% if lane_file_set.ivc_all %}
+ <tr>
+ <td>{{ lane_id }}</td>
+ <td>
+ <a href="{{ lane_file_set.ivc_all.get_absolute_url }}">
+ <img height="84" width="126" alt="Lane {{lane_id }} IVC All"
+ src="{{ lane_file_set.ivc_all.get_absolute_url }}"/></a>
+ </td>
+ <td>
+ <a href="{{ lane_file_set.ivc_call.get_absolute_url }}">
+ <img height="84" width="126" alt="Lane {{lane_id }} IVC Call"
+ src="{{ lane_file_set.ivc_call.get_absolute_url }}"/>
+ </a>
+ </td>
+ <td>
+ <a href="{{ lane_file_set.ivc_percent_base.get_absolute_url }}">
+ <img height="84" width="126" alt="Lane {{lane_id }} IVC % Base"
+ src="{{ lane_file_set.ivc_percent_base.get_absolute_url }}"/>
+ </a>
+ </td>
+ <td>
+ <a href="{{ lane_file_set.ivc_percent_all.get_absolute_url }}">
+ <img height="84" width="126" alt="Lane {{lane_id }} IVC % Base All"
+ src="{{ lane_file_set.ivc_percent_all.get_absolute_url }}"/>
+ </a>
+ </td>
+ <td>
+ <a href="{{ lane_file_set.ivc_percent_call.get_absolute_url }}">
+ <img height="84" width="126"
+ alt="Lane {{lane_id }} IVC % Base Called"
+ src="{{ lane_file_set.ivc_percent_call.get_absolute_url }}"/>
+ </a>
+ </td>
+ </tr>
+ {% endif %}
+ {% endfor %}
+ </tbody>
+ </table>
+ {% endif %}
+ {% endfor %}
+ </div>
+ </div>
+</div>
+<!-- end flowcell_detail -->
+{% endblock %}
--- /dev/null
+{% load staticfiles %}
+<div class="flowcell_identity" typeof="libns:IlluminaFlowcell" resource="{{flowcell.get_absolute_url}}">
+ <h2>About this Flowcell</h2>
+ <b>Flowcell</b>:
+ <a href="{{flowcell.get_absolute_url}}"><span property="libns:flowcell_id">{{flowcell.flowcell_id}}</span></a>{% if user.is_staff %}<a href="{{flowcell.get_admin_url}}"><img class="icon_button" src="{% static "admin/img/icon_changelink.gif" %}" alt="Edit"/></a>{% endif%}
+ <br/>
+ <div rel="libns:sequenced_by">
+ <div typeof="libns:Sequencer"
+ about="{{flowcell.sequencer.get_absolute_url}}">
+ <b>Instrument</b>:
+ <span property="libns:sequencer_name">{{ flowcell.sequencer.name }}</span>
+ {% if flowcell.sequencer.instrument_name %}
+ (<span property="libns:sequencer_instrument">{{ flowcell.sequencer.instrument_name}}</span>)
+ {% endif %}
+ <br/>
+ <b>Instrument Model</b>:
+ <span property="libns:sequencer_model">{{flowcell.sequencer.model}}</span>
+ <br/>
+ </div>
+ </div>
+ {% for datarun in flowcell.datarun_set.all %}
+ <b>Image Analysis</b>:
+ <span property="libns:image_software">{{datarun.image_software}}</span>
+ <span property="libns:image_version">{{datarun.image_version}}</span><br/>
+ <b>Base Caller</b>:
+ <span property="libns:basecall_software">{{datarun.basecall_software}}</span>
+ <span property="libns:basecall_version">{{datarun.basecall_version}}</span><br/>
+ <b>Alignment</b>:
+ <span property="libns:alignment_software">{{datarun.alignment_software}}</span>
+ <span property="libns:alignment_version">{{datarun.alignment_version}}</span><br/>
+ {% endfor %}
+ <b>Run Date</b>:
+ <span property="libns:date" content="{{flowcell.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd:dateTime">{{ flowcell.run_date }}</span><br/>
+ <b>Type</b>:
+ <span property="libns:flowcell_type">{{flowcell.flowcell_type}}</span><br/>
+ <b>Read Length</b>:
+ <span property="libns:read_length" datatype="xsd:integer">{{flowcell.read_length}}</span><br/>
+ <b>Control Lane</b>:
+ <span property="libns:control_lane">{{flowcell.control_lane}}</span><br/>
+
+ <b>Notes</b>:
+ <pre property="libns:flowcell_notes">{{flowcell.notes}}</pre>
+ </div>
--- /dev/null
+{% extends "base_site.html" %}
+{% load humanize i18n %}
+{% load staticfiles %}
+{% block extrahead %}
+ <!-- App Stuff -->
+ <link type="text/css" rel="stylesheet" href="{% static "css/app.css" %}"/>
+ <script type="text/javascript" src="{% static "js/jquery.min.js" %}"></script>
+
+ {% block additional_javascript %}
+ {% endblock %}
+{% endblock %}
+
+{% block content %}
+<div id="lane_detail" class="htswdetail" typeof="libns:IlluminaLane" resource="{{lane.get_absolute_url}}">
+ <div rel="libns:flowcell" resource="{{flowcell.get_absolute_url}}">
+ {% include "experiments/flowcell_header.html" %}
+ </div>
+ <div class="flowcell_lane_detail">
+ <h2>About this lane</h2>
+ <b>Lane</b>:
+ <span property="libns:lane_number">{{lane.lane_number}}</span><br/>
+ <b>pM</b>:
+ <span property="libns:pM" datatype="xsd:decimal">{{ lane.pM }}</span><br/>
+ {% if lane.cluster_estimate %}
+ <b>Cluster Estimate</b>:
+ <span property="libns:cluster_estimate" datatype="xsd:decimal"
+ content="{{lane.cluster_estimate}}">{{ lane.cluster_estimate|intcomma }}</span><br/>{% endif %}
+ {% if lane.status %}
+ <b>Lane Status</b>:
+ <span property="libns:status">{{ lane.status }}</span><br/>{% endif %}
+ {% if lane.comment %}
+ <b>Comments</b>:
+ <span property="libns:comment">{{ lane.comment }}</span><br/>{% endif %}
+ </div>
+ <hr/>
+ {% include "sample_header.html" %}
+ <hr/>
+ <div class="htsw_flowcell_ivc">
+ {% for run in flowcell.datarun_set.all %}
+ <h2>Run {{ run.runfolder_name }}</h2>
+ <table>
+ <thead>
+ <tr>
+ <td>Lane</td>
+ <td>IVC All</td>
+ <td>IVC Call</td>
+ <td>IVC Percent Base</td>
+ <td>IVC Percent Base All</td>
+ <td>IVC Percent Base Called</td>
+ </tr>
+ </thead>
+ <tbody>
+ {% for run, lane_number, lane_file_set in filtered_dataruns %}
+ {% if lane_file_set.ivc_all %}
+ <tr>
+ <td>{{lane_number}}</td>
+ <td>
+ <a href="{{ lane_file_set.ivc_all.get_absolute_url }}">
+ <img height="84" width="126" alt="Lane {{lane_id }} IVC All"
+ src="{{ lane_file_set.ivc_all.get_absolute_url }}"/></a>
+ </td>
+ <td>
+ <a href="{{ lane_file_set.ivc_call.get_absolute_url }}">
+ <img height="84" width="126" alt="Lane {{lane_id }} IVC Call"
+ src="{{ lane_file_set.ivc_call.get_absolute_url }}"/>
+ </a>
+ </td>
+ <td>
+ <a href="{{ lane_file_set.ivc_percent_base.get_absolute_url }}">
+ <img height="84" width="126" alt="Lane {{lane_id }} IVC % Base"
+ src="{{ lane_file_set.ivc_percent_base.get_absolute_url }}"/>
+ </a>
+ </td>
+ <td>
+ <a href="{{ lane_file_set.ivc_percent_all.get_absolute_url }}">
+ <img height="84" width="126" alt="Lane {{lane_id }} IVC % Base All"
+ src="{{ lane_file_set.ivc_percent_all.get_absolute_url }}"/>
+ </a>
+ </td>
+ <td>
+ <a href="{{ lane_file_set.ivc_percent_call.get_absolute_url }}">
+ <img height="84" width="126"
+ alt="Lane {{lane_id }} IVC % Base Called"
+ src="{{ lane_file_set.ivc_percent_call.get_absolute_url }}"/>
+ </a>
+ </td>
+ </tr>
+ {% else %}
+ <tr><td colspan="6">No data</td></tr>
+ {% endif %}
+ {% endfor %}
+ </tbody>
+ </table>
+ {% endfor %}
+ </div>
+</div>
+
+{% endblock %}
--- /dev/null
+{% if data_run_list %}
+ <table>
+ {% for run in data_run_list %}
+ <tr>
+ <td>{{run.run_folder}}</td>
+ <td><a href="fcsheet/{{run.fcid}}">sheet</td>
+ <td><a href="started/{{run.fcid}}">started email</td>
+ <td><a href="finished/{{run.fcid}}">finished email</td>
+ </tr>
+ {% endfor %}
+ </table>
+{% else %}
+ <p>No data runs are available.</p>
+{% endif %}
--- /dev/null
+{% extends "base_site.html" %}
+{% load humanize i18n %}
+{% load staticfiles %}
+{% block extrahead %}
+ <!-- App Stuff -->
+ <link type="text/css" rel="stylesheet" href="{% static "css/app.css" %}" />
+ <script type="text/javascript" src="{% static "js/jquery.min.js" %}"></script>
+
+ {% block additional_javascript %}
+ {% endblock %}
+{% endblock %}
+
+{% block content %}
+ <h1>Sequencer</h1>
+ <dl about="{{sequencer.get_absolute_url}}" typeof="libns:sequencer">
+ <dt>Name</dt>
+ <dl property="libns:sequencer_name">{{sequencer.name}}</dl>
+ <dt>Instrument Name</dt>
+ <dl property="libns:insrument_name">{{sequencer.instrument_name}}</dl>
+ <dt>Model</dt>
+ <dl property="libns:model">{{sequencer.model}}</dl>
+ <dt>Comment</dt>
+ <dl></dl>
+ </dl>
+{% endblock %}
--- /dev/null
+<p>
+The following libraries are on the flowcell {{ flowcell.flowcell_id }}
+which is a {{ flowcell.read_length }} base pair {% if flowcell.paired_end %}paired end{% else %}single ended{% endif %} flowcell.
+</p>
+<p>{% for lane in lanes %}
+Lane #{{ lane.lane_number }} :
+<a href="https://jumpgate.caltech.edu/library/{{lane.library.id}}">
+{{ lane.library.id }}</a>
+{{ lane.library.library_name }}<br/>
+{% endfor %}</p>
+<p>
+The data should be available at the following link when
+the pipeline finishes, probably in about {{ finish_low.days }} to {{ finish_high.days }}
+days from {{ now|date:"D, M d Y" }}
+</p>
+<p>
+<a href="https://jumpgate.caltech.edu/runfolders/{{ flowcell.sequencer}}/">
+https://jumpgate.caltech.edu/runfolders/{{ flowcell.sequencer }}
+</a></p>
--- /dev/null
+The following libraries are on the flowcell {{ flowcell.flowcell_id }}
+which is a {{ flowcell.read_length }} base pair {% if flowcell.paired_end %}paired end{% else %}single ended{% endif %} flowcell.
+
+Lane : (Library Id) Library Name (Cluster Estimate)
+{% for lane in lanes %}
+Lane #{{ lane.lane_number }} : ({{ lane.library.id }}) {{ lane.library.library_name }} ({{ lane.cluster_estimate }})
+ https://jumpgate.caltech.edu/library/{{ lane.library.id }}
+{% endfor %}
+
+The raw data should be available at the following link when the
+pipeline finishes, probably in about {{ finish_low.days }} to {{ finish_high.days }}
+days from {{ now|date:"D, M d Y" }}
+
+https://jumpgate.caltech.edu/runfolders/{{ flowcell.sequencer}}
+
+Username: gec
+Password: gecilluminadata
+
+- Jumpgate
+++ /dev/null
-{% if run_f %}
- <ul>
- RUN FOLDER: <li>{{ run_f.run_folder }}</li>
- </ul>
-{% else %}
- <p>Run folder not found.</p>
-{% endif %}
+++ /dev/null
-{% extends "base.html" %}
-{% load i18n %}
-
-{% block breadcrumbs %}
-<div class="breadcrumbs">
- <a href="/admin">{% trans 'Home' %}</a> ›
- <a href="/admin/experiments">Experiments</a> ›
- <a href="/admin/experiments/flowcell">flowcell</a> ›
- <a href="{{ flowcell.get_admin_url }}">{{ flowcell.flowcell_id }}</a>
-</div>
-{% endblock %}
-
-{% block content %}
-{% if warnings %}
-<hr/>
-<p>
-{% for user_admin_url, username in warnings %}
-Warning: User <a href="{{ user_admin_url}}">{{ username }}</a> has no
-email address <br/>
-{% endfor %}
-{% endif %}
-</p>
-{% for to, subject, body, sending in emails %}
-<hr/>
-{% if sending %}<b>Message:</b> {{ sending }}<br/>{% endif %}
-<b>From:</b> {{ from }}<br/>
-<b>To:</b> {{ to }}<br/>
-<b>Subject:</b> {{ subject }}<br/>
-<pre>
-{{ body }}
-</pre>
-{% endfor %}<hr/>
-<form method="get">
-<label for="bcc">BCC {% for m in site_managers %}{{ m }} {% endfor %}</label>
-<input type="checkbox" id="bcc" name="bcc" checked="on"/><br/>
-<input type="hidden" name="send" value="1"/>
-<input type="submit" value="Send Email"/>
-{% endblock %}
\ No newline at end of file
+++ /dev/null
-<html><head><title>{{ fc.flowcell_id }} - GA SEQUENCING (SOLEXA) LOG</title>
-<style type="text/css">
-<!--
-TD
- {
- color:black;
- font-size:9pt;
- font-face:Arial;
- }
--->
-</style>
-</head><body>
-{% if fc %}
-<table border="1" cellspacing="1">
-<tr><td colspan=2 nowrap><b>GA SEQUENCING (SOLEXA) LOG</b></td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td>Date Run Started</td><td colspan=2>{{ fc.run_date }}</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td>Cluster station used</td><td colspan=2 nowrap>{{ fc.cluster_station.name }}</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td>GA used</td><td colspan=2 nowrap>{{ fc.sequencer.name }}</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-
-<tr><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td>Flowcell number</td><td colspan=2 nowrap>{{ fc.flowcell_id }}</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td>Number of Tiles per Lane</td><td>100</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td>Number of Cycles</td><td>{{ fc.read_length }}</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td><font point-size="9" face="Arial"><b>SAMPLE INFORMATION</b><font></td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
-<tr><td> </td><td>FC#</td><td> </td><td> </td><td> </td><td> </td><td> </td><td colspan=2 nowrap>FC bar code</td></tr>
-
-<tr><td valign=middle nowrap>Lane</td>
-{% for lane in fc.lane_set.all %}
-<td>{{ lane.lane_number }}</td>
-{% endfor %}
-</tr>
-<tr><td valign=middle nowrap>Solexa Library Number</td>
-{% for lane in fc.lane_set.all %}
-<td bgcolor=#CCFFCC>{{ lane.library.id }}</td>
-{% endfor %}
-</tr>
-
-<tr><td valign=middle nowrap>Sample Name</td>
-{% for lane in fc.lane_set.all %}
-<td bgcolor=#CCFFCC>{{ lane.library.library_name }}</td>
-{% endfor %}
-</tr>
-
-<tr><td valign=middle nowrap>Organism</td>
-{% for lane in fc.lane_set.all %}
-<td bgcolor=#CCFFCC>{{ lane.library.library_species.scientific_name }}</td>
-{% endfor %}
-</tr>
-
-<tr><td valign=middle nowrap>Submitter</td>
-{% for lane in fc.lane_set.all %}
-<td bgcolor=#CCFFCC>{{ lane.library.made_for }}</td>
-{% endfor %}
-</tr>
-
-
-<tr><td valign=middle nowrap>First time run?</td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td><td bgcolor=#CCFFCC></td></tr>
-
-<tr><td valign=middle nowrap>Gel Cut Size (bp)</td>
-{% for lane in fc.lane_set.all %}
-<td bgcolor=#CCFFCC>{{ lane.library.gel_cut_size }}</td>
-{% endfor %}
-</tr>
-
-<tr><td valign=middle nowrap>Template Concentration (ng/ul)</td>
-{% for lane in fc.lane_set.all %}
-<td bgcolor=#CCFFCC>{{ lane.library.undiluted_concentration }}</td>
-{% endfor %}
-</tr>
-
-<tr><td valign=middle nowrap>Run Concentration (pM)</td>
-{% for lane in fc.lane_set.all %}
-<td bgcolor=#CCFFCC>{{ lane.pM }}</td>
-{% endfor %}
-</tr>
-
-</table>
-
-{% else %}
- <p>Flowcell object missing. Can't create sheet.</p>
-{% endif %}
-
-</body></html
+++ /dev/null
-{% extends "base_site.html" %}
-{% load staticfiles %}
-{% load humanize i18n %}
-{% block extrahead %}
- <!-- App Stuff -->
- <link type="text/css" rel="stylesheet" href="{% static "css/app.css" %}" />
- <script type="text/javascript" src="{% static "js/jquery.min.js" %}"></script>
-
- {% block additional_javascript %}
- {% endblock %}
-{% endblock %}
-
-{% block content %}
-<div>
- {% include "experiments/flowcell_header.html" %}
- <div class="htswdetail" typeof="libns:IlluminaFlowcell" resource="{{flowcell.get_absolute_url}}">
- <h2>Lanes</h2>
- <table>
- <thead>
- <tr>
- <td>Lane</td>
- <td>Library ID</td>
- <td>Library Name</td>
- <td>Species</td>
- <td>Comment</td>
- </tr>
- </thead>
- <tbody>
- {% for lane in lanes %}
- <tr>
- <td rel="libns:has_lane">
- <a href="{{lane.get_absolute_url}}" typeof="libns:IlluminaLane">
- <span property="libns:lane_number">{{lane.lane_number}}</span>
- </a>
- </td>
- <td rel="libns:library"
- about="{{lane.get_absolute_url}}"
- resource="{{lane.library.get_absolute_url}}">
- <a typeof="libns:Library" href="{{lane.library.get_absolute_url}}">
- <span property="libns:library_id"
- >{{lane.library.id}}</span></a>
- {% if user.is_staff %}
- <a href="{{lane.library.get_admin_url}}">
- <img class="icon_button"
- src="{% static "admin/img/icon_changelink.gif" %}"/>
- </a>{% endif %}
- </td>
- <td>
- <a href="{{lane.library.get_absolute_url}}">
- <span property="libns:name"
- about="{{lane.library.get_absolute_url}}"
- >{{lane.library.library_name}}</span>
- </a>
- </td>
- <td about="{{lane.library.get_absolute_url}}" rel="libns:species">
- <a href="{{lane.library.library_species.get_absolute_url}}"
- typeof="libns:Species">
- <span property="libns:species_name">{{ lane.library.library_species.scientific_name }}</span></a>
- </td>
- <td about="{{lane.get_absolute_url}}">
- <span property="libns:comment">{{lane.comment}}</span>
- </td>
- </tr>
- {% endfor %}
- </tbody>
- </table>
- <div class="htsw_flowcell_ivc">
- {% for run in flowcell.datarun_set.all %}
- <h2>Run {{ run.runfolder_name }}</h2>
- {% if run.lane_files %}
- <table>
- <thead>
- <tr>
- <td>Lane</td>
- <td>IVC All</td>
- <td>IVC Call</td>
- <td>IVC Percent Base</td>
- <td>IVC Percent Base All</td>
- <td>IVC Percent Base Called</td>
- </tr>
- </thead>
- <tbody>
- {% for lane_id, lane_file_set in run.lane_files.items %}
- {% if lane_file_set.ivc_all %}
- <tr>
- <td>{{ lane_id }}</td>
- <td>
- <a href="{{ lane_file_set.ivc_all.get_absolute_url }}">
- <img height="84" width="126" alt="Lane {{lane_id }} IVC All"
- src="{{ lane_file_set.ivc_all.get_absolute_url }}"/></a>
- </td>
- <td>
- <a href="{{ lane_file_set.ivc_call.get_absolute_url }}">
- <img height="84" width="126" alt="Lane {{lane_id }} IVC Call"
- src="{{ lane_file_set.ivc_call.get_absolute_url }}"/>
- </a>
- </td>
- <td>
- <a href="{{ lane_file_set.ivc_percent_base.get_absolute_url }}">
- <img height="84" width="126" alt="Lane {{lane_id }} IVC % Base"
- src="{{ lane_file_set.ivc_percent_base.get_absolute_url }}"/>
- </a>
- </td>
- <td>
- <a href="{{ lane_file_set.ivc_percent_all.get_absolute_url }}">
- <img height="84" width="126" alt="Lane {{lane_id }} IVC % Base All"
- src="{{ lane_file_set.ivc_percent_all.get_absolute_url }}"/>
- </a>
- </td>
- <td>
- <a href="{{ lane_file_set.ivc_percent_call.get_absolute_url }}">
- <img height="84" width="126"
- alt="Lane {{lane_id }} IVC % Base Called"
- src="{{ lane_file_set.ivc_percent_call.get_absolute_url }}"/>
- </a>
- </td>
- </tr>
- {% endif %}
- {% endfor %}
- </tbody>
- </table>
- {% endif %}
- {% endfor %}
- </div>
- </div>
-</div>
-<!-- end flowcell_detail -->
-{% endblock %}
+++ /dev/null
-{% load staticfiles %}
-<div class="flowcell_identity" typeof="libns:IlluminaFlowcell" resource="{{flowcell.get_absolute_url}}">
- <h2>About this Flowcell</h2>
- <b>Flowcell</b>:
- <a href="{{flowcell.get_absolute_url}}"><span property="libns:flowcell_id">{{flowcell.flowcell_id}}</span></a>{% if user.is_staff %}<a href="{{flowcell.get_admin_url}}"><img class="icon_button" src="{% static "admin/img/icon_changelink.gif" %}" alt="Edit"/></a>{% endif%}
- <br/>
- <div rel="libns:sequenced_by">
- <div typeof="libns:Sequencer"
- about="{{flowcell.sequencer.get_absolute_url}}">
- <b>Instrument</b>:
- <span property="libns:sequencer_name">{{ flowcell.sequencer.name }}</span>
- {% if flowcell.sequencer.instrument_name %}
- (<span property="libns:sequencer_instrument">{{ flowcell.sequencer.instrument_name}}</span>)
- {% endif %}
- <br/>
- <b>Instrument Model</b>:
- <span property="libns:sequencer_model">{{flowcell.sequencer.model}}</span>
- <br/>
- </div>
- </div>
- {% for datarun in flowcell.datarun_set.all %}
- <b>Image Analysis</b>:
- <span property="libns:image_software">{{datarun.image_software}}</span>
- <span property="libns:image_version">{{datarun.image_version}}</span><br/>
- <b>Base Caller</b>:
- <span property="libns:basecall_software">{{datarun.basecall_software}}</span>
- <span property="libns:basecall_version">{{datarun.basecall_version}}</span><br/>
- <b>Alignment</b>:
- <span property="libns:alignment_software">{{datarun.alignment_software}}</span>
- <span property="libns:alignment_version">{{datarun.alignment_version}}</span><br/>
- {% endfor %}
- <b>Run Date</b>:
- <span property="libns:date" content="{{flowcell.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd:dateTime">{{ flowcell.run_date }}</span><br/>
- <b>Type</b>:
- <span property="libns:flowcell_type">{{flowcell.flowcell_type}}</span><br/>
- <b>Read Length</b>:
- <span property="libns:read_length" datatype="xsd:integer">{{flowcell.read_length}}</span><br/>
- <b>Control Lane</b>:
- <span property="libns:control_lane">{{flowcell.control_lane}}</span><br/>
-
- <b>Notes</b>:
- <pre property="libns:flowcell_notes">{{flowcell.notes}}</pre>
- </div>
+++ /dev/null
-{% extends "base_site.html" %}
-{% load humanize i18n %}
-{% load staticfiles %}
-{% block extrahead %}
- <!-- App Stuff -->
- <link type="text/css" rel="stylesheet" href="{% static "css/app.css" %}"/>
- <script type="text/javascript" src="{% static "js/jquery.min.js" %}"></script>
-
- {% block additional_javascript %}
- {% endblock %}
-{% endblock %}
-
-{% block content %}
-<div id="lane_detail" class="htswdetail" typeof="libns:IlluminaLane" resource="{{lane.get_absolute_url}}">
- <div rel="libns:flowcell" resource="{{flowcell.get_absolute_url}}">
- {% include "experiments/flowcell_header.html" %}
- </div>
- <div class="flowcell_lane_detail">
- <h2>About this lane</h2>
- <b>Lane</b>:
- <span property="libns:lane_number">{{lane.lane_number}}</span><br/>
- <b>pM</b>:
- <span property="libns:pM" datatype="xsd:decimal">{{ lane.pM }}</span><br/>
- {% if lane.cluster_estimate %}
- <b>Cluster Estimate</b>:
- <span property="libns:cluster_estimate" datatype="xsd:decimal"
- content="{{lane.cluster_estimate}}">{{ lane.cluster_estimate|intcomma }}</span><br/>{% endif %}
- {% if lane.status %}
- <b>Lane Status</b>:
- <span property="libns:status">{{ lane.status }}</span><br/>{% endif %}
- {% if lane.comment %}
- <b>Comments</b>:
- <span property="libns:comment">{{ lane.comment }}</span><br/>{% endif %}
- </div>
- <hr/>
- {% include "sample_header.html" %}
- <hr/>
- <div class="htsw_flowcell_ivc">
- {% for run in flowcell.datarun_set.all %}
- <h2>Run {{ run.runfolder_name }}</h2>
- <table>
- <thead>
- <tr>
- <td>Lane</td>
- <td>IVC All</td>
- <td>IVC Call</td>
- <td>IVC Percent Base</td>
- <td>IVC Percent Base All</td>
- <td>IVC Percent Base Called</td>
- </tr>
- </thead>
- <tbody>
- {% for run, lane_number, lane_file_set in filtered_dataruns %}
- {% if lane_file_set.ivc_all %}
- <tr>
- <td>{{lane_number}}</td>
- <td>
- <a href="{{ lane_file_set.ivc_all.get_absolute_url }}">
- <img height="84" width="126" alt="Lane {{lane_id }} IVC All"
- src="{{ lane_file_set.ivc_all.get_absolute_url }}"/></a>
- </td>
- <td>
- <a href="{{ lane_file_set.ivc_call.get_absolute_url }}">
- <img height="84" width="126" alt="Lane {{lane_id }} IVC Call"
- src="{{ lane_file_set.ivc_call.get_absolute_url }}"/>
- </a>
- </td>
- <td>
- <a href="{{ lane_file_set.ivc_percent_base.get_absolute_url }}">
- <img height="84" width="126" alt="Lane {{lane_id }} IVC % Base"
- src="{{ lane_file_set.ivc_percent_base.get_absolute_url }}"/>
- </a>
- </td>
- <td>
- <a href="{{ lane_file_set.ivc_percent_all.get_absolute_url }}">
- <img height="84" width="126" alt="Lane {{lane_id }} IVC % Base All"
- src="{{ lane_file_set.ivc_percent_all.get_absolute_url }}"/>
- </a>
- </td>
- <td>
- <a href="{{ lane_file_set.ivc_percent_call.get_absolute_url }}">
- <img height="84" width="126"
- alt="Lane {{lane_id }} IVC % Base Called"
- src="{{ lane_file_set.ivc_percent_call.get_absolute_url }}"/>
- </a>
- </td>
- </tr>
- {% else %}
- <tr><td colspan="6">No data</td></tr>
- {% endif %}
- {% endfor %}
- </tbody>
- </table>
- {% endfor %}
- </div>
-</div>
-
-{% endblock %}
+++ /dev/null
-{% if data_run_list %}
- <table>
- {% for run in data_run_list %}
- <tr>
- <td>{{run.run_folder}}</td>
- <td><a href="fcsheet/{{run.fcid}}">sheet</td>
- <td><a href="started/{{run.fcid}}">started email</td>
- <td><a href="finished/{{run.fcid}}">finished email</td>
- </tr>
- {% endfor %}
- </table>
-{% else %}
- <p>No data runs are available.</p>
-{% endif %}
+++ /dev/null
-{% extends "base_site.html" %}
-{% load humanize i18n %}
-{% load staticfiles %}
-{% block extrahead %}
- <!-- App Stuff -->
- <link type="text/css" rel="stylesheet" href="{% static "css/app.css" %}" />
- <script type="text/javascript" src="{% static "js/jquery.min.js" %}"></script>
-
- {% block additional_javascript %}
- {% endblock %}
-{% endblock %}
-
-{% block content %}
- <h1>Sequencer</h1>
- <dl about="{{sequencer.get_absolute_url}}" typeof="libns:sequencer">
- <dt>Name</dt>
- <dl property="libns:sequencer_name">{{sequencer.name}}</dl>
- <dt>Instrument Name</dt>
- <dl property="libns:insrument_name">{{sequencer.instrument_name}}</dl>
- <dt>Model</dt>
- <dl property="libns:model">{{sequencer.model}}</dl>
- <dt>Comment</dt>
- <dl></dl>
- </dl>
-{% endblock %}
+++ /dev/null
-<p>
-The following libraries are on the flowcell {{ flowcell.flowcell_id }}
-which is a {{ flowcell.read_length }} base pair {% if flowcell.paired_end %}paired end{% else %}single ended{% endif %} flowcell.
-</p>
-<p>{% for lane in lanes %}
-Lane #{{ lane.lane_number }} :
-<a href="https://jumpgate.caltech.edu/library/{{lane.library.id}}">
-{{ lane.library.id }}</a>
-{{ lane.library.library_name }}<br/>
-{% endfor %}</p>
-<p>
-The data should be available at the following link when
-the pipeline finishes, probably in about {{ finish_low.days }} to {{ finish_high.days }}
-days from {{ now|date:"D, M d Y" }}
-</p>
-<p>
-<a href="https://jumpgate.caltech.edu/runfolders/{{ flowcell.sequencer}}/">
-https://jumpgate.caltech.edu/runfolders/{{ flowcell.sequencer }}
-</a></p>
+++ /dev/null
-The following libraries are on the flowcell {{ flowcell.flowcell_id }}
-which is a {{ flowcell.read_length }} base pair {% if flowcell.paired_end %}paired end{% else %}single ended{% endif %} flowcell.
-
-Lane : (Library Id) Library Name (Cluster Estimate)
-{% for lane in lanes %}
-Lane #{{ lane.lane_number }} : ({{ lane.library.id }}) {{ lane.library.library_name }} ({{ lane.cluster_estimate }})
- https://jumpgate.caltech.edu/library/{{ lane.library.id }}
-{% endfor %}
-
-The raw data should be available at the following link when the
-pipeline finishes, probably in about {{ finish_low.days }} to {{ finish_high.days }}
-days from {{ now|date:"D, M d Y" }}
-
-https://jumpgate.caltech.edu/runfolders/{{ flowcell.sequencer}}
-
-Username: gec
-Password: gecilluminadata
-
-- Jumpgate
projects / htsworkflow.git / commitdiff