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<!DOCTYPE html>
<html lang="en" ng-app="sraExplorerApp">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="An experimental interface for exploring the Sequence Read Archive">
<meta name="author" content="Phil Ewels">
<title>SRA Explorer</title>
<!-- Framework CSS -->
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" rel="stylesheet">
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.1/css/font-awesome.min.css">
<!-- SRA-explorer styles -->
<style type="text/css">
/* Core structural setup */
body {
padding-top: 50px;
}
/* Styles for little clear button on search fields */
.form-control-clear, .form-control-clear:hover, .form-control-clear:focus, .form-control-clear:active {
pointer-events: auto;
text-decoration: none;
cursor: pointer;
color: #999;
z-index: 4;
}
.form-control-clear:hover, .form-control-clear:focus, .form-control-clear:active {
color: #666;
}
/* Make button links have proper styling */
a[ng-click]{
cursor: pointer;
}
/* Page Header */
.jumbotron {
margin-top: 30px;
}
.jumbotron h1 {
margin-top: 0;
}
.jumbotron h1 a {
color: #333;
text-decoration: none;
}
/* Saved datasets */
#savedDatasets pre {
overflow-x: auto;
}
#savedDatasets pre code {
font-size: 10px;
white-space: pre;
}
/* Seqera Platform stuff */
#fullSeqeraPlatform_table_wrapper {
overflow: auto;
width: 100%;
max-height: 300px;
}
#seqera-icon {
height: 1.6rem;
width: 1.6rem;
margin: 0 0.3rem -0.3rem 0;
filter: saturate(0) brightness(0);
opacity: 0.3;
transform: 300ms;
}
.active #seqera-icon {
filter: saturate(1) brightness(1);
opacity: 1;
}
</style>
<!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body ng-controller="searchCtrl">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<a class="navbar-brand" href="#" ng-click="returnToHomeButton()">SRA-Explorer</a>
<a href="#" class="btn navbar-btn" style="float:right;" ng-class="savedResults.length == 0 ? 'disabled btn-default' : 'btn-primary'" ng-click="checkoutButton()"><span class="glyphicon glyphicon-shopping-cart"></span> <span ng-bind="savedResults.length"></span> saved datasets</a>
</div>
</div>
<div class="container">
<div class="jumbotron">
<h1><a href="#" ng-click="returnToHomeButton()">SRA Explorer</a></h1>
<p>This tool aims to make datasets within the Sequence Read Archive more accessible.</p>
<form class="form-horizontal" role="search">
<div class="form-group form-group-lg">
<label class="col-sm-2 control-label" for="searchText">Search for:</label>
<div class="col-sm-10">
<div class="input-group">
<div class="has-feedback has-clear">
<input ng-model="searchText" id="searchText" type="text" class="form-control" placeholder="Enter accession number" required>
<a class="glyphicon glyphicon-remove-sign form-control-feedback form-control-clear" ng-click="searchText = ''" ng-show="searchText.length"></a>
</div>
<div class="input-group-btn">
<button ng_click="search()" class="btn btn-default btn-lg" type="submit"><span class="glyphicon glyphicon-search"></span></button>
</div>
</div>
</div>
</div>
<div class="form-group">
<label class="col-sm-2 control-label" for="maxResults">Max Results</label>
<div class="col-sm-2">
<input type="number" max="500" class="form-control" id="maxResults" ng-model="maxResults" value="100" required>
</div>
<label class="col-sm-2 control-label" for="retstart">Start At Record</label>
<div class="col-sm-2">
<input type="number" class="form-control" id="retstart" ng-model="retstart" value="0" required>
</div>
</div>
<span id="helpBlock" class="help-block">
Need inspiration? Try
<code ng-click="searchText='GSE30567'; search()" style="cursor:pointer;">GSE30567</code>,
<code ng-click="searchText='SRP043510'; search()" style="cursor:pointer;">SRP043510</code>,
<code ng-click="searchText='PRJEB8073'; search()" style="cursor:pointer;">PRJEB8073</code>,
<code ng-click="searchText='ERP009109'; search()" style="cursor:pointer;">ERP009109</code> or
<code ng-click="searchText='human liver miRNA'; search()" style="cursor:pointer;">human liver miRNA</code>.
</span>
</form>
</div>
<div class="alert alert-info" ng-show="savedResults.length > 0 && results.length == 0 && !showSaved">
You have {{ savedResults.length }} datasets in your collection.
<a href="#" ng-click="checkoutButton()">View saved datasets</a>.
</div>
<p ng-show="loadingSpinner" class="text-center"><span class="glyphicon glyphicon-refresh fa-spin"></span> Loading..</p>
<div ng-show="results.length > 0">
<hr>
<div class="alert alert-info">
Select relevant datasets and click <em>add to collection</em>.
When you're finished, view all saved datasets with the button in the top right of the
page, where you can copy the SRA URLs.
</div>
<p>Showing <span ng-bind="filteredResults.length" class="badge"></span> results.</p>
<button class="pull-right btn btn-primary" ng-class="{disabled: selectedItems == 0}" ng-click="saveDatasets()">Add <span ng-bind="selectedItems">0</span> to collection</button>
<form class="form-inline" role="search">
<div class="form-group">
<label for="filterText">Filter results:</label>
<div class="input-group">
<div class="form-group has-feedback has-clear">
<input ng-model="filterText" id="filterText" type="text" class="form-control" placeholder="Enter search term">
<a class="glyphicon glyphicon-remove-sign form-control-feedback form-control-clear" ng-click="filterText = ''" ng-show="filterText.length"></a>
</div>
<div class="input-group-btn">
<button type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">All Fields <span class="caret"></span></button>
<ul class="dropdown-menu dropdown-menu-right">
<li class="active"><a href="#">All Fields</a></li>
<li><a href="#">Title</a></li>
<li><a href="#">Accession</a></li>
<li><a href="#">Instrument</a></li>
</ul>
</div>
</div>
</div>
</form>
<hr>
<div class="table-responsive"><table class="table table-striped table-hover">
<thead>
<tr>
<th><input type="checkbox" ng-model="selectAll" ng-click="checkAll()"></th>
<th><a ng-click="sortType = 'title'; sortReverse = !sortReverse">
Title
<span ng-show="sortType == 'title' && !sortReverse" class="fa fa-caret-down"></span>
<span ng-show="sortType == 'title' && sortReverse" class="fa fa-caret-up"></span>
</a></th>
<th><a ng-click="sortType = 'accession'; sortReverse = !sortReverse">
Accession
<span ng-show="sortType == 'accession' && !sortReverse" class="fa fa-caret-down"></span>
<span ng-show="sortType == 'accession' && sortReverse" class="fa fa-caret-up"></span>
</a></th>
<th><a ng-click="sortType = 'platform'; sortReverse = !sortReverse">
Instrument
<span ng-show="sortType == 'platform' && !sortReverse" class="fa fa-caret-down"></span>
<span ng-show="sortType == 'platform' && sortReverse" class="fa fa-caret-up"></span>
</a></th>
<th><a ng-click="sortType = 'total_bases'; sortReverse = !sortReverse">
Total Bases (Mb)
<span ng-show="sortType == 'total_bases' && !sortReverse" class="fa fa-caret-down"></span>
<span ng-show="sortType == 'total_bases' && sortReverse" class="fa fa-caret-up"></span>
</a></th>
<th><a ng-click="sortType = 'createdate'; sortReverse = !sortReverse">
Date Created
<span ng-show="sortType == 'createdate' && !sortReverse" class="fa fa-caret-down"></span>
<span ng-show="sortType == 'createdate' && sortReverse" class="fa fa-caret-up"></span>
</a></th>
</tr>
</thead>
<tbody>
<tr ng-repeat="x in results | orderBy:sortType:sortReverse | filter:filterText as filteredResults" ng-click="rowClicked(x)" ng-class="{ success: x.selected }">
<td><input type="checkbox" ng-checked="x.selected" ng-click="toggleRow($event, x)"></td>
<td>{{ x.title }}</td>
<td><a href="https://www.ncbi.nlm.nih.gov/sra/?term={{ x.accession }}" target="_blank">{{ x.accession }}</a></td>
<td>{{ x.platform }}</td>
<td>{{ x.total_bases }}</td>
<td>{{ x.createdate | date:'dd MMM yyyy' }}</td>
</tr>
</tbody>
</table></div>
</div>
<!-- Saved datasets -->
<div id="savedDatasets" ng-show="showSaved" class="animate-show">
<h2>
<span ng-bind="savedResults.length"></span> Saved Datasets
<button ng-show="savedResults.length > 0" ng-click="returnSaved()" class="btn btn-default" style="float:right;">Remove all from collection and send to search results</button>
</h2>
<div>
<!-- Nav tabs -->
<ul class="nav nav-tabs" role="tablist">
<li class="active"><a href="#fastq_tabcontent" aria-controls="fastq_tabcontent" role="tab" data-toggle="tab">FastQ Downloads</a></li>
<li><a href="#sra_tabcontent" aria-controls="sra_tabcontent" role="tab" data-toggle="tab">SRA Downloads</a></li>
<li><a href="#full_metadata_tabcontent" aria-controls="full_metadata_tabcontent" role="tab" data-toggle="tab">Full Metadata</a></li>
<li><a href="#seqera_platform_tabcontent" aria-controls="seqera_platform_tabcontent" role="tab" data-toggle="tab">
<svg id="seqera-icon" width="250" height="250" viewBox="0 0 250 250" fill="none" xmlns="http://www.w3.org/2000/svg">
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Seqera Platform
</a></li>
</ul>
<div class="tab-content">
<div role="tabpanel" class="tab-pane fade in active" id="fastq_tabcontent">
<div ng-show="savedResults.length > 0" class="panel-group" id="fastqAccordion" role="tablist" aria-multiselectable="true">
<p><br>To download FastQ files directly, sra-explorer queries the <a href="https://www.ebi.ac.uk/ena" target="_blank" rel="nofollow">ENA</a> for each SRA run accession number.</p>
<div class="panel panel-default">
<div class="panel-heading" role="tab">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#fastqAccordion" href="#fastqURLs">Raw FastQ Download URLs</a>
</h4>
</div>
<div id="fastqURLs" class="panel-collapse collapse" role="tabpanel">
<div class="panel-body">
<p>The following is a list of links to download the selected SRA runs as FastQ from the ENA.</p>
<p>
<button class="btn btn-sm btn-default btn-copy" data-clipboard-target="#fastqURLs_content"><span class="glyphicon glyphicon-copy"></span> Copy</button>
<button class="btn btn-sm btn-default btn-download" ng-click="download_contents('#fastqURLs_content', 'sra_explorer_fastq_urls.txt')"><span class="glyphicon glyphicon-download-alt"></span> Download</button>
</p>
<p ng-show="savedResultsENAaccessions.length < savedResults.length" class="text-center"><span class="glyphicon glyphicon-refresh fa-spin"></span> Loading <span class="badge"><span ng-bind="savedResultsENAaccessions.length"></span> / <span ng-bind="savedResults.length"></span></span>..</p>
<pre ng-show="savedResultsENAfastq.length > 0" id="fastqURLs_content"><code ng-repeat="x in savedResultsENAfastq">{{ x.fastq_url }}{{ nlChr }}</code></pre>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading" role="tab">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#fastqAccordion" href="#fastqURLs_bashCURL">Bash script for downloading FastQ files</a>
</h4>
</div>
<div id="fastqURLs_bashCURL" class="panel-collapse collapse" role="tabpanel">
<div class="panel-body">
<p>This list of bash <code>curl</code> commands to download each SRA run FastQ file from the ENA, and save with a nicer filename, with the cleaned dataset title appended.</p>
<p>
<button class="btn btn-sm btn-default btn-copy" data-clipboard-target="#fastqURLs_bashCURL_content"><span class="glyphicon glyphicon-copy"></span> Copy</button>
<button class="btn btn-sm btn-default btn-download" ng-click="download_contents('#fastqURLs_bashCURL_content', 'sra_explorer_fastq_download.sh')"><span class="glyphicon glyphicon-download-alt"></span> Download</button>
</p>
<p ng-show="savedResultsENAaccessions.length < savedResults.length" class="text-center"><span class="glyphicon glyphicon-refresh fa-spin"></span> Loading <span class="badge"><span ng-bind="savedResultsENAaccessions.length"></span> / <span ng-bind="savedResults.length"></span></span>..</p>
<pre ng-show="savedResultsENAfastq.length > 0" id="fastqURLs_bashCURL_content"><code>#!/usr/bin/env bash</code><code ng-repeat="x in savedResultsENAfastq">{{ nlChr }}curl -L {{ x.fastq_url }} -o {{ x.fastq_niceFilename }}</code></pre>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading" role="tab">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#fastqAccordion" href="#fastqURLs_aspera">Aspera commands for downloading FastQ files</a>
</h4>
</div>
<div id="fastqURLs_aspera" class="panel-collapse collapse" role="tabpanel">
<div class="panel-body">
<p>This list of bash <code>ascp</code> commands to download each FastQ file from the ENA using the <a href="https://downloads.asperasoft.com/en/downloads/8?list" target="_blank" rel="nofollow">Aspera download tool</a>.</p>
<form class="form-horizontal">
<div class="form-group">
<label for="inputEmail3" class="col-sm-2 control-label">ascp openssh key path</label>
<div class="col-sm-10">
<div class="input-group">
<input type="text" class="form-control" id="ascp_openssh_location" ng-model="ascp_openssh_location">
<span class="input-group-btn">
<button class="btn btn-default" type="button" ng-click="set_ascp_openssh_location('linux')"><i class="fa fa-linux" aria-hidden="true"></i> Linux</button>
<button class="btn btn-default" type="button" ng-click="set_ascp_openssh_location('osx')"><i class="fa fa-apple" aria-hidden="true"></i> OSX</button>
</span>
</div>
</div>
</div>
<div class="form-group">
<label for="inputEmail3" class="col-sm-2 control-label">Rename files?</label>
<div class="col-sm-10">
<label class="radio-inline">
<input type="radio" ng-model="ascp_append_mv" ng-value="true"> Append <code>mv</code> command to rename downloaded files
</label>
<label class="radio-inline">
<input type="radio" ng-model="ascp_append_mv" ng-value="false"> Don't rename files
</label>
</div>
</div>
</form>
<p>
<button class="btn btn-sm btn-default btn-copy" data-clipboard-target="#fastqURLs_aspera_content"><span class="glyphicon glyphicon-copy"></span> Copy</button>
<button class="btn btn-sm btn-default btn-download" ng-click="download_contents('#fastqURLs_aspera_content', 'sra_explorer_fastq_aspera_download.sh')"><span class="glyphicon glyphicon-download-alt"></span> Download</button>
</p>
<p ng-show="savedResultsENAaccessions.length < savedResults.length" class="text-center"><span class="glyphicon glyphicon-refresh fa-spin"></span> Loading <span class="badge"><span ng-bind="savedResultsENAaccessions.length"></span> / <span ng-bind="savedResults.length"></span></span>..</p>
<pre ng-show="savedResultsENAfastq.length > 0" id="fastqURLs_aspera_content"><code>#!/usr/bin/env bash</code><code ng-repeat="x in savedResultsENAfastq">{{ nlChr }}ascp -QT -l 300m -P33001 -i {{ ascp_openssh_location }} {{ x.fastq_asperaurl }} .<span ng-show="ascp_append_mv"> && mv {{ x.fastq_filename }} {{ x.fastq_niceFilename }}</span></code></pre>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading" role="tab">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#fastqAccordion" href="#fastqURLs_bcbio">bcbio project file for FastQ downloads</a>
</h4>
</div>
<div id="fastqURLs_bcbio" class="panel-collapse collapse" role="tabpanel">
<div class="panel-body">
<p>This list of URLs is followed by a nicer filename. This is suitable for use with <a href="https://bcbio-nextgen.readthedocs.io/en/latest/" target="_blank">bcbio-nextgen</a> analysis pipelines.</p>
<p>
<button class="btn btn-sm btn-default btn-copy" data-clipboard-target="#fastqURLs_bcbio_content"><span class="glyphicon glyphicon-copy"></span> Copy</button>
<button class="btn btn-sm btn-default btn-download" ng-click="download_contents('#fastqURLs_bcbio_content', 'sra_explorer_bcbio.txt')"><span class="glyphicon glyphicon-download-alt"></span> Download</button>
</p>
<p ng-show="savedResultsENAaccessions.length < savedResults.length" class="text-center"><span class="glyphicon glyphicon-refresh fa-spin"></span> Loading <span class="badge"><span ng-bind="savedResultsENAaccessions.length"></span> / <span ng-bind="savedResults.length"></span></span>..</p>
<pre ng-show="savedResultsENAfastq.length > 0" id="fastqURLs_bcbio_content"><code>samplename,description</code><code ng-repeat="x in savedResultsENAfastq">{{ nlChr }}{{ x.fastq_url }},{{ x.fastq_niceFilename }}</code></pre>
</div>
</div>
</div>
</div>
</div>
<div role="tabpanel" class="tab-pane fade" id="sra_tabcontent">
<div ng-show="savedResults.length > 0" class="panel-group" id="sraAccordion" role="tablist" aria-multiselectable="true">
<p><br>These download links are automatically generated based on the URL schema of the NCBI SRA.</p>
<div class="panel panel-default">
<div class="panel-heading" role="tab">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#sraAccordion" href="#ftpURLs">Raw SRA Download URLs</a>
</h4>
</div>
<div id="ftpURLs" class="panel-collapse collapse" role="tabpanel">
<div class="panel-body">
<p>The following is a list of links to download the selected SRA files.</p>
<p>
<button class="btn btn-sm btn-default btn-copy" data-clipboard-target="#ftpURLs_content"><span class="glyphicon glyphicon-copy"></span> Copy</button>
<button class="btn btn-sm btn-default btn-download" ng-click="download_contents('#ftpURLs_content', 'sra_explorer_sra_urls.txt')"><span class="glyphicon glyphicon-download-alt"></span> Download</button>
</p>
<pre id="ftpURLs_content"><code ng-repeat="x in savedResults">{{ x.sra_url }}{{ nlChr }}</code></pre>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading" role="tab">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#sraAccordion" href="#ftpURLs_bashCURL">
Bash script for downloading SRA files (nice filenames)
</a>
</h4>
</div>
<div id="ftpURLs_bashCURL" class="panel-collapse collapse" role="tabpanel">
<div class="panel-body">
<p>This list of bash <code>curl</code> commands to download each SRA file and save with a nicer filename, with the cleaned dataset title appended.</p>
<p>
<button class="btn btn-sm btn-default btn-copy" data-clipboard-target="#ftpURLs_bashCURL_content"><span class="glyphicon glyphicon-copy"></span> Copy</button>
<button class="btn btn-sm btn-default btn-download" ng-click="download_contents('#ftpURLs_bashCURL_content', 'sra_explorer_sra_download.sh')"><span class="glyphicon glyphicon-download-alt"></span> Download</button>
</p>
<pre id="ftpURLs_bashCURL_content"><code>#!/usr/bin/env bash</code><code ng-repeat="x in savedResults">{{ nlChr }}curl -L {{ x.sra_url }} -o {{ x.sra_niceFilename }}</code></pre>
</div>
</div>
</div>
</div>
</div>
<div role="tabpanel" class="tab-pane fade" id="full_metadata_tabcontent">
<div ng-show="savedResults.length > 0" class="panel-group" id="fullMetaAccordion" role="tablist" aria-multiselectable="true">
<p><br>These files contain the metadata used by SRA-Explorer for downstream use. Note that each SRA record is repeated for every ENA FastQ entry.</p>
<div class="panel panel-default">
<div class="panel-heading" role="tab">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#fullMetaAccordion" href="#fullTSV">TSV</a>
</h4>
</div>
<div id="fullTSV" class="panel-collapse collapse" role="tabpanel">
<div class="panel-body">
<p>The following is a TSV (tab separated values) file with all metadata fields for the selected samples.</p>
<p>
<button class="btn btn-sm btn-default btn-copy" data-clipboard-target="#fullTSV_content"><span class="glyphicon glyphicon-copy"></span> Copy</button>
<button class="btn btn-sm btn-default btn-download" ng-click="download_contents('#fullTSV_content', 'sra_explorer_metadata.tsv')"><span class="glyphicon glyphicon-download-alt"></span> Download</button>
</p>
<p ng-show="savedResultsENAaccessions.length < savedResults.length" class="text-center"><span class="glyphicon glyphicon-refresh fa-spin"></span> Loading <span class="badge"><span ng-bind="savedResultsENAaccessions.length"></span> / <span ng-bind="savedResults.length"></span></span>..</p>
<pre ng-show="savedResultsENAfastq.length > 0" id="fullTSV_content"><code>Accession{{ tabChr }}Title{{ tabChr }}Platform{{ tabChr }}Total bases{{ tabChr }}Create date{{ tabChr }}SRA URL{{ tabChr }}SRA filename{{ tabChr }}SRA nice filename{{ tabChr }}FastQ URL{{ tabChr }}FastQ Aspera URL{{ tabChr }}FastQ filename{{ tabChr }}FastQ nice filename</code><code ng-repeat="x in savedResultsENAfastq">{{ nlChr }}{{ x.accession }}{{ tabChr }}{{ x.title }}{{ tabChr }}{{ x.platform }}{{ tabChr }}{{ x.total_bases }}{{ tabChr }}{{ x.createdate }}{{ tabChr }}{{ x.sra_url }}{{ tabChr }}{{ x.accession }}.sra{{ tabChr }}{{ x.sra_niceFilename }}{{ tabChr }}{{ x.fastq_url }}{{ tabChr }}{{ x.fastq_asperaurl }}{{ tabChr }}{{ x.fastq_filename }}{{ tabChr }}{{ x.fastq_niceFilename }}</code></pre>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading" role="tab">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#fullMetaAccordion" href="#fullJSON">JSON</a>
</h4>
</div>
<div id="fullJSON" class="panel-collapse collapse" role="tabpanel">
<div class="panel-body">
<p>The following is a JSON file with all metadata fields for the selected samples.</p>
<p>
<button class="btn btn-sm btn-default btn-copy" data-clipboard-target="#fullJSON_content"><span class="glyphicon glyphicon-copy"></span> Copy</button>
<button class="btn btn-sm btn-default btn-download" ng-click="download_contents('#fullJSON_content', 'sra_explorer_metadata.json')"><span class="glyphicon glyphicon-download-alt"></span> Download</button>
</p>
<p ng-show="savedResultsENAaccessions.length < savedResults.length" class="text-center"><span class="glyphicon glyphicon-refresh fa-spin"></span> Loading <span class="badge"><span ng-bind="savedResultsENAaccessions.length"></span> / <span ng-bind="savedResults.length"></span></span>..</p>
<pre ng-show="savedResultsENAfastq.length > 0" id="fullJSON_content"><code>{{ savedResultsENAfastq | json }}</code></pre>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading" role="tab">
<h4 class="panel-title">
<a role="button" data-toggle="collapse" data-parent="#fullMetaAccordion" href="#fullYAML">YAML</a>
</h4>
</div>
<div id="fullYAML" class="panel-collapse collapse" role="tabpanel">
<div class="panel-body">
<p>The following is a YAML file with all metadata fields for the selected samples.</p>
<p>
<button class="btn btn-sm btn-default btn-copy" data-clipboard-target="#fullYAML_content"><span class="glyphicon glyphicon-copy"></span> Copy</button>
<button class="btn btn-sm btn-default btn-download" ng-click="download_contents('#fullYAML_content', 'sra_explorer_metadata.yaml')"><span class="glyphicon glyphicon-download-alt"></span> Download</button>
</p>
<p ng-show="savedResultsENAaccessions.length < savedResults.length" class="text-center"><span class="glyphicon glyphicon-refresh fa-spin"></span> Loading <span class="badge"><span ng-bind="savedResultsENAaccessions.length"></span> / <span ng-bind="savedResults.length"></span></span>..</p>
<pre ng-show="savedResultsENAfastq.length > 0" id="fullYAML_content"><code>{{ savedResultsENAfastqYAML }}</code></pre>
</div>
</div>
</div>
</div>
</div>
<div role="tabpanel" class="tab-pane fade" id="seqera_platform_tabcontent">
<p><br><a href="https://nextflow.io/" target="_blank">Nextflow</a> and the
<a href="https://seqera.io/platform/" target="_blank">Seqera Platform</a>
enable scalable and reproducible scientific workflows.
Many Nextflow pipelines use a sample sheet <code>.csv</code> file to handle input metadata.
This can be supplied within Seqera Platform as a <a href="https://docs.seqera.io/platform/latest/data/datasets" target="_blank">Dataset</a>.
SRA-Explorer allows metadata from public sequencing data to be saved as a Dataset in Seqera Platform.
</p>
<p>Note that SRA records are repeated for every ENA FastQ entry.</p>
<div class="panel panel-default">
<div class="panel-heading" role="tab">
<h4 class="panel-title">
<a role="button" href="#seqera_platform">Seqera Platform</a>
</h4>
</div>
<div id="seqera_platform">
<div class="panel-body">
<p>Send all metadata to Seqera Platform as a saved Dataset, which you can use as an input when launching pipelines.</p>
<form id="seqera_platform_form" class="form-horizontal">
<div class="form-group">
<div class="col-sm-9" ng-show="!seqeraplatform.credentials_valid">
<div class="alert alert-info" style="padding: 6px 12px;">
Please connect your Seqera Platform account to proceed.
</div>
</div>
<div class="col-sm-2" ng-show="seqeraplatform.credentials_valid">
<label class="sr-only" for="sp_organisation">Organisation</label>
<select class="form-control" ng-model="seqeraplatform.selected_org" ng-change="update_seqera_org()"> id="sp_organisation">
<option ng-repeat="(orgId, orgName) in seqeraplatform.orgs" value="{{ orgId }}">{{ orgName }}</option>
</select>
</div>
<div class="col-sm-2" ng-show="seqeraplatform.credentials_valid">
<label class="sr-only" for="sp_workspace_id">Workspace</label>
<select class="form-control" ng-model="seqeraplatform.workspace_id" id="sp_workspace_id">
<option ng-repeat="(wsId, wsName) in seqeraplatform.workspaces[seqeraplatform.selected_org]" value="{{ wsId }}">{{ wsName }}</option>
</select>
</div>
<div class="col-sm-2" ng-show="seqeraplatform.credentials_valid">
<label class="sr-only" for="sp_name">Dataset name</label>
<input type="text" class="form-control" ng-model="seqeraplatform.name" id="sp_name" placeholder="Dataset name">
</div>
<div class="col-sm-3" ng-show="seqeraplatform.credentials_valid">
<label class="sr-only" for="sp_description">Dataset description</label>
<input type="text" class="form-control" ng-model="seqeraplatform.description" id="sp_description" placeholder="Dataset description">
</div>
<div class="col-sm-3 text-right">
<button type="submit" class="btn btn-default" data-toggle="modal" data-target="#seqeraPlatformConnectionModal">
<span class="glyphicon glyphicon-log-in"></span> Connect
</button>
<button type="submit" class="btn btn-primary" disabled ng-click="save_seqeraplatform(seqeraplatform)" ng-disabled="!seqeraplatform.credentials_valid || seqeraplatform.workspace_id == ''">
<span class="glyphicon glyphicon-send"></span> Add Dataset
</button>
</div>
</div>
</form>
<div ng-show="seqeraplatform.messages.length > 0" class="alert" ng-class="{'alert-success': !seqeraplatform.hasError, 'alert-danger': seqeraplatform.hasError }">
<p ng-repeat="x in seqeraplatform.messages"><ng-bind-html ng-bind-html="x"></ng-bind-html></p>
</div>
<p ng-show="savedResultsENAaccessions.length < savedResults.length" class="text-center"><span class="glyphicon glyphicon-refresh fa-spin"></span> Loading <span class="badge"><span ng-bind="savedResultsENAaccessions.length"></span> / <span ng-bind="savedResults.length"></span></span>..</p>
<div id="fullSeqeraPlatform_table_wrapper">
<table ng-show="savedResultsENAfastq.length > 0" id="fullSeqeraPlatform_content" class="table table-bordered table-hover table-condensed small">
<thead>
<tr>
<th>Accession</th>
<th>Title</th>
<th>Platform</th>
<th>Total bases</th>
<th>Create date</th>
<th>SRA URL</th>
<th>SRA filename</th>
<th>SRA nice filename</th>
<th>FastQ URL</th>
<th>FastQ Aspera URL</th>
<th>FastQ filename</th>
<th>FastQ nice filename</th>
</tr>
</thead>
<tbody>
<tr ng-repeat="x in savedResultsENAfastq">
<td>{{ x.accession }}</td>
<td>{{ x.title }}</td>
<td>{{ x.platform }}</td>
<td>{{ x.total_bases }}</td>
<td>{{ x.createdate }}</td>
<td>{{ x.sra_url }}</td>
<td>{{ x.accession }}.sra</td>
<td>{{ x.sra_niceFilename }}</td>
<td>{{ x.fastq_url }}</td>
<td>{{ x.fastq_asperaurl }}</td>
<td>{{ x.fastq_filename }}</td>
<td>{{ x.fastq_niceFilename }}</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p ng-show="summaryURL">Query URL = <code ng-bind="summaryURL"></code></p>
</div><!-- /.container -->
<hr>
<div class="container footer text-muted">
<p>
SRA-Explorer was written by <a href="http://phil.ewels.co.uk">Phil Ewels</a>.
Source code is available under a GNU GPLv3 licence at <a href="https://github.com/ewels/sra-explorer">https://github.com/ewels/sra-explorer</a>.
</p>
<p>
Here a lot? It might be worth taking a look at <a href="https://github.com/ewels/sra-explorer#alternatives">some alternative tools</a>..
</p>
</div>
<!-- Modal -->
<div class="modal fade" id="seqeraPlatformConnectionModal" tabindex="-1" role="dialog" aria-labelledby="seqeraPlatformConnectionModalLabel">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>
<h4 class="modal-title" id="seqeraPlatformConnectionModalLabel">Seqera Platform Connection</h4>
</div>
<div class="modal-body">
<p>To connect to the Seqera Platform, please enter your credentials:</p>
<div class="form-group">
<label for="sp_frontend_url">Seqera Platform URL</label>
<input type="text" class="form-control" ng-model="seqeraplatform.frontend_url" id="sp_frontend_url" placeholder="Platform URL" value="https://cloud.seqera.io/">
<p class="help-block small">If using Seqera Cloud, leave as <code>https://cloud.seqera.io/</code>. If using a custom Seqera Enterprise installation, enter your base Seqera Platform URL.</p>
</div>
<div class="form-group">
<label for="sp_api_base">API Base URL</label>
<input type="text" class="form-control" ng-model="seqeraplatform.api_base" id="sp_api_base" placeholder="API Base URL" value="https://api.cloud.seqera.io/">
<p class="help-block small">If using Seqera Cloud, leave as <code>https://api.cloud.seqera.io/</code>. If using a custom Seqera Enterprise installation, enter your base API route.</p>
</div>
<div class="form-group">
<label for="sp_access_token">Access Token</label>
<input type="password" class="form-control" ng-model="seqeraplatform.access_token" id="sp_access_token" placeholder="Access Token">
<p class="help-block small">Create an Access Token at <a href="https://cloud.seqera.io/tokens" target="_blank">https://cloud.seqera.io/tokens</a> (or in your enterprise installation).</p>
</div>
<p class="small">
You may save these details in a browser cookie, so that you do not need to enter them every time.
This is stored on your device only. <strong>Do not use this feature on a shared computer.</strong>
</p>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-default" ng-click="save_seqera_credentials(seqeraplatform, false)">Close and use this time</button>
<button type="button" class="btn btn-primary" ng-click="save_seqera_credentials(seqeraplatform, true)">Save in browser cookie</button>
</div>
</div>
</div>
</div>
<!-- Core JavaScript -->
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/js/bootstrap.min.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/angularjs/1.4.9/angular.min.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/angularjs/1.4.9/angular-sanitize.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.5.10/clipboard.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/js-yaml/3.12.2/js-yaml.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/FileSaver.js/1.3.8/FileSaver.js"></script>
<!-- SRA-Explorer Code -->
<script type="text/javascript">
var app = angular.module("sraExplorerApp", ['ngSanitize']);
app.controller("searchCtrl", function($scope, $http) {
$scope.searchText = "";
$scope.maxResults = 100;
$scope.retstart = 0;
$scope.summaryURL = 0;
$scope.loadingSpinner = 0;
$scope.sortType = '';
$scope.results = [];
$scope.savedResults = [];
$scope.savedResultsENAaccessions = [];
$scope.savedResultsENAfastq = [];
$scope.savedResultsENAfastqYAML = '';
$scope.showSaved = false;
$scope.tabChr = "\t";
$scope.nlChr = "\n";
$scope.ascp_openssh_location = '$HOME/.aspera/connect/etc/asperaweb_id_dsa.openssh';
$scope.ascp_append_mv = true;
$scope.seqeraplatform = {
'frontend_url': 'https://cloud.seqera.io/',
'api_base': 'https://api.cloud.seqera.io/',
'access_token': '',
'user_id': '',
'workspace_id': '',
'name': '',
'description': '',
'credentials_valid': false,
'orgs': {},
'workspaces': {},
'selected_org': '',
'messages': [],
'hasError': false
};
// Load saved Seqera Platform connection details from cookie (not localstorage)
if (document.cookie.indexOf('seqeraPlatformFrontendURL') > -1) {
var frontend_url = document.cookie.split('; ').find(row => row.startsWith('seqeraPlatformFrontendURL=')).split('=')[1];
if(frontend_url && frontend_url != ''){
$scope.seqeraplatform.frontend_url = frontend_url;
}
}
if (document.cookie.indexOf('seqeraPlatformAPIBase') > -1) {
var api_base = document.cookie.split('; ').find(row => row.startsWith('seqeraPlatformAPIBase=')).split('=')[1];
if(api_base && api_base != ''){
$scope.seqeraplatform.api_base = api_base;
}
}
if (document.cookie.indexOf('seqeraPlatformAccessToken') > -1) {
var access_token = document.cookie.split('; ').find(row => row.startsWith('seqeraPlatformAccessToken=')).split('=')[1];
if(access_token && access_token != ''){
$scope.seqeraplatform.access_token = access_token;
}
console.log("Loaded Seqera Platform credentials from cookie");
}
$scope.seqeraplatform.credentials_valid = are_seqera_platform_credentials_valid();
$scope.search = function() { searchSRA($scope.searchText); };
/* Search Function */
function searchSRA (string) {
$scope.showSaved = false;
$scope.loadingSpinner = 1;
$scope.results = [];
var searchURL = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&usehistory=y&retmode=json&term='+string;
$http.get(searchURL).success(function(s_response) {
if(s_response.esearchresult.querytranslation){
$scope.searchText = s_response.esearchresult.querytranslation;
}
var webenv = s_response.esearchresult.webenv;
var querykey = s_response.esearchresult.querykey;
var retmax = $scope.maxResults;
var retstart = $scope.retstart;
var resultsURL = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=sra&retmode=json&query_key='+querykey+'&WebEnv='+webenv+'&retstart='+retstart+'&retmax='+retmax;
$scope.summaryURL = resultsURL;
$http.get(resultsURL).success(function(response) {
$scope.loadingSpinner = 0;
// Parse the stupid embedded XML
angular.forEach(response.result, function(value, key) {
// Exp XML
expXMLraw = '<document>'+value.expxml+'</document>';
parser = new DOMParser();
expXML = parser.parseFromString(expXMLraw,"text/xml");
expJSON = xmlToJson(expXML);
if(expJSON.document.Summary){
exp = expJSON.document.Summary;
value.expxml = exp;
}
// Runs
runsXMLraw = '<document>'+value.runs+'</document>';
parser = new DOMParser();
runsXML = parser.parseFromString(runsXMLraw,"text/xml");
runsJSON = xmlToJson(runsXML);
if(runsJSON.document.Run){
value.runs = runsJSON.document.Run;
// If only one SRR, make it an array
if(!Array.isArray(value.runs)){
value.runs = [value.runs];
}
// Loop through each run result
for(var i = 0; i < value.runs.length; i++){
// Add results to scope
try {
var sra_cleanTitle = value.expxml.Title.text.replace(/[^a-z0-9\._\-]/gi, '_').replace(/_+/g, '_');
$scope.results.push({
'title': value.expxml.Title.text,
'accession': value.runs[i].attributes.acc,
'platform': value.expxml.Platform.attributes.instrument_model,
'total_bases': Math.round(value.runs[i].attributes.total_bases / 100000),
'createdate': Date.parse(value.createdate),
'cleanTitle': sra_cleanTitle,
'sra_url': "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/"+value.runs[i].attributes.acc.substring(0,3)+"/"+value.runs[i].attributes.acc.substring(0,6)+"/"+value.runs[i].attributes.acc+"/"+value.runs[i].attributes.acc+".sra",
'sra_niceFilename': value.runs[i].attributes.acc+'_'+sra_cleanTitle+'.sra'
});
} catch(e){
console.log(e);
console.log({key: value});
}
};
}
});
// console.log(response.result);
});
});
}
// Toggle row selection checkboxes
$scope.toggleRow = function($event, obj) {
$event.stopPropagation();
obj.selected = !obj.selected;
}
$scope.rowClicked = function(obj) {
obj.selected = !obj.selected;
};
$scope.checkAll = function () {
angular.forEach($scope.filteredResults, function (item) {
item.selected = $scope.selectAll;
});
};
$scope.$watch('filteredResults', function(items){
var selectedItems = 0;
angular.forEach(items, function(item){
selectedItems += item.selected ? 1 : 0;
});
$scope.selectedItems = selectedItems;
}, true);
// Save datasets
$scope.saveDatasets = function() {
angular.forEach($scope.filteredResults, function(item){
if(item.selected){
var alreadyAdded = false;
for (i=0; i<$scope.savedResults.length; i++){
if (item['accession'] == $scope.savedResults[i]['accession']){
alreadyAdded = true;
}
}
if(!alreadyAdded){
$scope.savedResults.push( angular.copy(item) );
}
}
});
};
// Show saved datasets
$scope.checkoutButton = function(){
// Clear search results and show saved
$scope.results = [];
$scope.summaryURL = 0;
$scope.loadingSpinner = 0;
$scope.showSaved = true;
$scope.fetchFastqENA();
}
// Show saved datasets
$scope.returnToHomeButton = function(){
// Clear search results and hide results again
$scope.showSaved = false;
$scope.results = [];
$scope.searchText = '';
}
// Send saved datasets back to table
$scope.returnSaved = function() {
// Clear search results and show saved
$scope.results = angular.copy( $scope.savedResults );
$scope.savedResults = [];
$scope.showSaved = false;
}
// Send saved datasets back to table
$scope.fetchFastqENA = function() {
if($scope.savedResultsENAaccessions.length < $scope.savedResults.length){
angular.forEach($scope.savedResults, function(value, key) {
if($scope.savedResultsENAaccessions.indexOf(value['accession']) === -1){
var ENAsearchURL = 'https://www.ebi.ac.uk/ena/portal/api/filereport?result=read_run&fields=fastq_ftp&format=JSON&accession='+value['accession'];
$http.get(ENAsearchURL).success(function(s_response) {
for (var i = 0; i < s_response.length; i++) {
var ftpFastQ = s_response[i]["fastq_ftp"];
if (ftpFastQ != undefined) {
// Paired-end FastQ files are given as a single result, need to split by ; character
var ftpFastQ_urls = ftpFastQ.split(';');
for(var j = 0; j < ftpFastQ_urls.length; j++){
// Save the accession now that we have some download filenames, so we know that this worked
if($scope.savedResultsENAaccessions.indexOf(value['accession']) === -1){
$scope.savedResultsENAaccessions.push(value['accession']);
}
var fname = ftpFastQ_urls[j].substring(ftpFastQ_urls[j].lastIndexOf('/')+1);
$scope.savedResultsENAfastq.push({
// Original SRA data
'title': value['title'],
'accession': value['accession'],
'cleanTitle': value['cleanTitle'],
'platform': value['platform'],
'total_bases': value['total_bases'],
'createdate': value['createdate'],
'sra_url': value['sra_url'],
'sra_niceFilename': value['sra_niceFilename'],
// New FastQ fields
'fastq_url': 'ftp://'+ftpFastQ_urls[j],
'fastq_asperaurl': ftpFastQ_urls[j].replace('ftp.sra.ebi.ac.uk/', 'era-fasp@fasp.sra.ebi.ac.uk:').replace('ftp.ebi.ac.uk/', 'era-fasp@fasp.ebi.ac.uk:'),
'fastq_filename': fname,
'fastq_niceFilename': value['accession']+'_'+value['cleanTitle']+fname.replace(value['accession'], '')
});
$scope.savedResultsENAfastqYAML = jsyaml.safeDump($scope.savedResultsENAfastq);
}
}
}
});
}
});
}
}
// Customise the ascp openssh location with buttons
$scope.set_ascp_openssh_location = function(loc){
if(loc == 'linux'){
$scope.ascp_openssh_location = '$HOME/.aspera/connect/etc/asperaweb_id_dsa.openssh';
}
if(loc == 'osx'){
$scope.ascp_openssh_location = '$HOME/Applications/Aspera\\ Connect.app/Contents/Resources/asperaweb_id_dsa.openssh';
}
}
// Download contents as a file
$scope.download_contents = function(target, filename){
var content = $(target).text();
var blob = new Blob([content], { type: "text/plain;charset=utf-8" });
saveAs(blob, filename);
}
// Save Seqera Platform API details to a cookie
$scope.save_seqera_credentials = function(sp, save_cookie) {
if(save_cookie){
console.log("Saving Seqera Platform API details to cookie");
// Expire in 1 month
var d = new Date();
d.setTime(d.getTime() + (30*24*60*60*1000));
var expires = "; expires="+d.toUTCString();
// Save cookies
document.cookie = "seqeraPlatformFrontendURL="+sp.frontend_url+expires;
document.cookie = "seqeraPlatformAPIBase="+sp.api_base+expires;
document.cookie = "seqeraPlatformAccessToken="+sp.access_token+expires;
}
// Set valid state
$scope.seqeraplatform.credentials_valid = are_seqera_platform_credentials_valid();
// Hide the modal
if($scope.seqeraplatform.credentials_valid){
$('#seqeraPlatformConnectionModal').modal('hide');
} else {
alert("Credentials seem invalid");
}
}
function are_seqera_platform_credentials_valid(){
// Check if we have valid credentials and fetch orgs / workspaces
if($scope.seqeraplatform.frontend_url && $scope.seqeraplatform.frontend_url != '' && $scope.seqeraplatform.api_base && $scope.seqeraplatform.api_base != '' && $scope.seqeraplatform.access_token && $scope.seqeraplatform.access_token != ''){
get_seqera_orgs_workspaces();
return true;
}
return false;
}
function has_workspace_permissions(roles){
let valid_roles = ['owner','admin','maintain','launch'];
for (var i = 0; i < valid_roles.length; i++) {
if(roles.indexOf(valid_roles[i]) > -1){
return true;
}
}
return false;
}
function get_seqera_orgs_workspaces(){
$scope.seqeraplatform.user_id = '';
$scope.seqeraplatform.orgs = {};
$scope.seqeraplatform.workspaces = {};
$scope.seqeraplatform.selected_org = '';
$scope.seqeraplatform.workspace_id = '';
// Get the User ID from Seqera API /user-info endpoint
var api_url_get_user = $scope.seqeraplatform.api_base.replace(/\/+$/, '')+'/user-info';
var headers = {
"Content-Type": "application/json",
"Authorization": "Bearer "+$scope.seqeraplatform.access_token
};
$http({
url: api_url_get_user,
headers: headers,
method: "GET"
}).then(function successCallback(sp_response) {
console.log("Got user:", sp_response);
$scope.seqeraplatform.user_id = sp_response.data.user.id;
// Now get orgs and workspaces
var api_url_get_orgs_workspaces = $scope.seqeraplatform.api_base.replace(/\/+$/, '')+'/user/'+$scope.seqeraplatform.user_id+'/workspaces';
$http({
url: api_url_get_orgs_workspaces,
headers: headers,
method: "GET"
}).then(function successCallback(sp_response) {
console.log('Got workspaces', sp_response);
angular.forEach(sp_response.data.orgsAndWorkspaces, function(ws, key) {
if(ws.workspaceId && has_workspace_permissions(ws.roles)){
$scope.seqeraplatform.orgs[ws.orgId] = ws.orgName;
if($scope.seqeraplatform.selected_org == ''){
$scope.seqeraplatform.selected_org = ws.orgId.toString();
$scope.seqeraplatform.workspace_id = ws.workspaceId.toString();
}
if(!(ws.orgId in $scope.seqeraplatform.workspaces)){
$scope.seqeraplatform.workspaces[ws.orgId] = {};
}
$scope.seqeraplatform.workspaces[ws.orgId][ws.workspaceId] = ws.workspaceName;
}
});
}, function errorCallback(sp_response) {
console.log("Error fetching Seqera Platform workspaces", sp_response);
$scope.seqeraplatform.messages.push('Error fetching Seqera Platform workspaces');
$scope.seqeraplatform.hasError = true;
$scope.seqeraplatform.credentials_valid = false;
});
}, function errorCallback(sp_response) {
console.log("Error fetching Seqera Platform orgs", sp_response);
$scope.seqeraplatform.messages.push('Error fetching Seqera Platform organizations');
$scope.seqeraplatform.hasError = true;
$scope.seqeraplatform.credentials_valid = false;
});