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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="Common reference genomes hosted on AWS S3">
<meta name="author" content="Philip Ewels">
<title>AWS iGenomes</title>
<!-- Bootstrap core CSS -->
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-alpha.6/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-rwoIResjU2yc3z8GV/NPeZWAv56rSmLldC3R/AZzGRnGxQQKnKkoFVhFQhNUwEyJ" crossorigin="anonymous">
<style type="text/css">
.mainbody {
padding: 50px 15px;
}
.subtitle {
font-weight: 200;
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pre {
background-color: #ededed;
border-radius: 5px;
padding: 20px;
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code {
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label {
font-weight: bold;
}
button, .local_code {
cursor: pointer;
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margin: 30px 0;
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position: relative;
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</style>
</head>
<body>
<div class="container mainbody">
<img title="AWS Programs for Research and Education" src="images/AWS_logo.png" class="hidden-lg-down float-lg-right">
<h1 class="display-1">AWS iGenomes</h1>
<h2 class="subtitle text-muted mb-5">Common reference genomes hosted on AWS S3</h2>
<p>This resource hosts commonly used bioinformatics reference genomes with the help
of a grant from <a href="https://aws.amazon.com/grants/">AWS Programs for Research and Education</a>.</p>
<p>In order to get the references, you need to sync the files from S3 to your EC2 environment.
This web page contains two tools to help you with that - a <a href="#sync-command-builder">command builder</a>
and a <a href="#command-line-script">command-line script</a>.
<p>For more information about this resource, please see the GitHub readme at
<a href="https://github.com/ewels/AWS-iGenomes">https://github.com/ewels/AWS-iGenomes</a>.</p>
<hr>
<h2><a name="sync-command-builder">Sync command builder</a></h2>
<p>Use the dropdown boxes below to build an AWS S3 sync command for your reference.</p>
<form>
<div class="row">
<div class="form-group col-sm-3">
<label for="genome">Genome</label>
<select class="form-control" id="genome">
<option value="">[ select ]</option>
<optgroup label="Common Genomes">
<option value="Homo_sapiens">Homo sapiens</option>
<option value="Mus_musculus">Mus Musculus</option>
<option value="Saccharomyces_cerevisiae">Saccharomyces cerevisiae</option>
</optgroup>
<optgroup label="All Genomes" id="all_genomes"></optgroup>
</select>
</div>
<div class="form-group col-sm-3">
<label for="source">Source</label>
<select class="form-control" id="source" disabled>
<option value="">Please select a genome</option>
</select>
</div>
<div class="form-group col-sm-3">
<label for="build">Build</label>
<select class="form-control" id="build" disabled>
<option value="">Please select a source</option>
</select>
</div>
<div class="form-group col-sm-3">
<label for="type">Type</label>
<select class="form-control" id="type" disabled>
<option value="">Please select a build</option>
</select>
</div>
</div>
<div class="row">
<div class="form-group col-sm-3">
<label for="region">Region</label>
<small class="text-muted">Currently just <code>eu-west-1</code></small>
<select class="form-control" id="region" disabled>
<option value="eu-west-1">eu-west-1</option>
</select>
</div>
<div class="form-group col-sm-9">
<label for="local">Local directory</label>
<small class="text-muted">Available variables:
<code class="local_code">{genome}</code>,
<code class="local_code">{source}</code>,
<code class="local_code">{build}</code>,
<code class="local_code">{type_path}</code>
</small>
<input type="text" class="form-control" id="local" value="./references/{genome}/{source}/{build}/{type_path}" style="font-family:Menlo,Monaco,Consolas,'Liberation Mono','Courier New',monospace;">
</div>
</div>
</form>
<h5>Bucket URL</h5>
<div class="prewrap" id="bucket_url_wrapper">
<button class="btn" data-clipboard-target="#bucket_url" disabled>Copy</button>
<pre><code id="bucket_url"><span class="text-muted">waiting for selection…</span></code></pre>
</div>
<h5>Sync command</h5>
<div class="prewrap" id="sync_command_wrapper">
<button class="btn" data-clipboard-target="#sync_command" disabled>Copy</button>
<pre><code id="sync_command"><span class="text-muted">waiting for selection…</span></code></pre>
</div>
<div id="manifest_accordion" role="tablist" aria-multiselectable="true">
<div class="card">
<div class="card-header" role="tab" id="manifest_heading">
<h6 class="mb-0">
<a data-toggle="collapse" data-parent="#manifest_accordion" href="#manifest_dropdown" aria-expanded="true" aria-controls="manifest_dropdown">
File list for selected download
</a>
</h6>
</div>
<div id="manifest_dropdown" class="collapse" role="tabpanel" aria-labelledby="manifest_heading">
<pre class="card-block mb-0" id="file_manifest">Loading file manifest..</pre>
</div>
</div>
</div>
<hr>
<h2><a name="command-line-script">Command-line Script</a></h2>
<p>You can use a bash script we've written which can be used to easily obtain reference genomes
where you need them. This builds the required command using either command-line prompts or
flags, then runs the sync command for you.</p>
<p>Note that you need to have the
<a href="http://docs.aws.amazon.com/cli/latest/userguide/installing.html" target="_blank">aws command line tools</a>
installed and set up with proper authentication.</p>
<h5 class="mt-4">Quick usage</h5>
<p>Paste this command in your terminal to download and run the script directly.</p>
<div class="prewrap">
<button class="btn btn-warning" data-clipboard-target="#aws_script_call">Copy</button>
<pre><code id="aws_script_call">curl -fsSL https://ewels.github.io/AWS-iGenomes/aws-igenomes.sh | bash</code></pre>
</div>
<h5 class="mt-4">Advanced usage</h5>
<p>You can save the script locally and run it with command-line flags as follows:</p>
<div class="prewrap">
<button class="btn btn-warning" data-clipboard-target="#aws_script_download">Copy</button>
<pre><code id="aws_script_download">curl -fsSL https://ewels.github.io/AWS-iGenomes/aws-igenomes.sh > aws-igenomes.sh</code></pre>
</div>
<pre><code>bash aws-igenomes.sh --help
<span class="text-muted">
USAGE: aws-igenomes.sh
[-g <genome name>]
[-s <source name>]
[-b <build name>]
[-t <reference type>]
[-o <output directory>]
[-d (dry run, no downloads)]
[-q (quiet mode, non-interactive)]
[-h (usage help)]
All command line flags are optional. If not specified
and not running in quiet-mode, the script will prompt
for input and show available options.
Please note that this script requires the AWS command
line tools to be installed and configured for authenticated
access.</span></code></pre>
<p><strong>Script source:</strong> <a href="https://github.com/ewels/AWS-iGenomes/blob/master/aws-igenomes.sh">https://github.com/ewels/AWS-iGenomes/blob/master/aws-igenomes.sh</a></p>
<p><strong>Script URL:</strong> <a href="aws-igenomes.sh">https://ewels.github.io/AWS-iGenomes/aws-igenomes.sh</a></p>
<p>If you have any questions or feature requests, please
<a href="https://github.com/ewels/AWS-iGenomes/issues">create an issue</a>.</p>
</div>
<div class="footer">
<div class="container">
This resource was developed by <a href="http://phil.ewels.co.uk">Phil Ewels</a>, a bioinformatician
at the <a href="https://ngisweden.scilifelab.se/">National Genomics Infrastructure</a> in Stockholm,
Sweden. It is based on the <a href="https://support.illumina.com/sequencing/sequencing_software/igenome.html">illumina iGenomes</a>
which has been added to with the help of <a href="https://www.uppmax.uu.se/">UPPMAX</a>.
S3 hosting fees are kindly covered by a grant supplied by Amazon.
<div class="row mt-4">
<div class="col-md-4 text-center"><a href="https://aws.amazon.com/grants/"><img title="AWS Programs for Research and Education" src="images/AWS_logo.png"></a></div>
<div class="col-md-4 text-center"><a href="http://www.scilifelab.se/"><img title="SciLifeLab" src="images/SciLifeLab_logo.png" class="sll-logo"></a></div>
<div class="col-md-4 text-center"><a href="https://ngisweden.scilifelab.se/"><img title="National Genomics Infrastructure" src="images/NGI_logo.png"></a></div>
</div>
</div>
</div>
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"Drosophila_melanogaster/Ensembl/BDGP5": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Drosophila_melanogaster/Ensembl/BDGP5.25": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Drosophila_melanogaster/Ensembl/BDGP6": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Drosophila_melanogaster/NCBI/build4.1": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Drosophila_melanogaster/NCBI/build5": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Drosophila_melanogaster/NCBI/build5.3": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Drosophila_melanogaster/NCBI/build5.41": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Drosophila_melanogaster/UCSC/dm3": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Drosophila_melanogaster/UCSC/dm6": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Enterobacteriophage_lambda/NCBI/1993-04-28": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Equus_caballus/Ensembl/EquCab2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Equus_caballus/NCBI/EquCab2.0": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Equus_caballus/UCSC/equCab2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Escherichia_coli_K_12_DH10B/Ensembl/EB1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Escherichia_coli_K_12_DH10B/NCBI/2008-03-17": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Escherichia_coli_K_12_MG1655/NCBI/2001-10-15": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Gallus_gallus/Ensembl/Galgal4": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Gallus_gallus/Ensembl/WASHUC2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Gallus_gallus/NCBI/build2.1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Gallus_gallus/NCBI/build3.1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Gallus_gallus/UCSC/galGal3": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Gallus_gallus/UCSC/galGal4": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Glycine_max/Ensembl/Gm01": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Homo_sapiens/Ensembl/GRCh37": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Homo_sapiens/GATK/b37": ["gatk"],
"Homo_sapiens/GATK/hg19": ["gatk"],
"Homo_sapiens/GATK/hg38": ["gatk"],
"Homo_sapiens/GATK/GRCh37": ["gatk"],
"Homo_sapiens/GATK/GRCh38": ["gatk"],
"Homo_sapiens/NCBI/build36.3": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Homo_sapiens/NCBI/build37.1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Homo_sapiens/NCBI/build37.2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Homo_sapiens/NCBI/GRCh38": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Homo_sapiens/NCBI/GRCh38Decoy": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Homo_sapiens/UCSC/hg18": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Homo_sapiens/UCSC/hg19": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Homo_sapiens/UCSC/hg38": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Macaca_mulatta/Ensembl/Mmul_1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Mus_musculus/Ensembl/GRCm38": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Mus_musculus/Ensembl/NCBIM37": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Mus_musculus/NCBI/build37.1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Mus_musculus/NCBI/build37.2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Mus_musculus/NCBI/GRCm38": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Mus_musculus/UCSC/mm10": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Mus_musculus/UCSC/mm9": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Mycobacterium_tuberculosis_H37RV/Ensembl/H37Rv.EB1": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Mycobacterium_tuberculosis_H37RV/NCBI/2001-09-07": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Oryza_sativa_japonica/Ensembl/IRGSP-1.0": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Oryza_sativa_japonica/Ensembl/MSU6": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Pan_troglodytes/Ensembl/CHIMP2.1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Pan_troglodytes/Ensembl/CHIMP2.1.4": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Pan_troglodytes/NCBI/build2.1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Pan_troglodytes/NCBI/build3.1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Pan_troglodytes/UCSC/panTro2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Pan_troglodytes/UCSC/panTro3": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Pan_troglodytes/UCSC/panTro4": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"PhiX/Illumina/RTA": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"PhiX/NCBI/1993-04-28": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Pseudomonas_aeruginosa_PAO1/NCBI/2000-09-13": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Rattus_norvegicus/Ensembl/RGSC3.4": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Rattus_norvegicus/Ensembl/Rnor_5.0": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Rattus_norvegicus/Ensembl/Rnor_6.0": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Rattus_norvegicus/NCBI/RGSC_v3.4": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Rattus_norvegicus/NCBI/Rnor_5.0": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Rattus_norvegicus/NCBI/Rnor_6.0": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Rattus_norvegicus/UCSC/rn4": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Rattus_norvegicus/UCSC/rn5": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Rattus_norvegicus/UCSC/rn6": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Rhodobacter_sphaeroides_2.4.1/NCBI/2005-10-07": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Saccharomyces_cerevisiae/Ensembl/EF2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Saccharomyces_cerevisiae/Ensembl/EF3": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Saccharomyces_cerevisiae/Ensembl/EF4": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Saccharomyces_cerevisiae/Ensembl/R64-1-1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Saccharomyces_cerevisiae/NCBI/build2.1": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Saccharomyces_cerevisiae/NCBI/build3.1": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Saccharomyces_cerevisiae/UCSC/sacCer2": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Saccharomyces_cerevisiae/UCSC/sacCer3": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Schizosaccharomyces_pombe/Ensembl/EF1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Schizosaccharomyces_pombe/Ensembl/EF2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Sorangium_cellulosum_So_ce_56/NCBI/2007-11-27": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Sorghum_bicolor/Ensembl/Sbi1": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Staphylococcus_aureus_NCTC_8325/NCBI/2006-02-13": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq"],
"Sus_scrofa/Ensembl/Sscrofa10.2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Sus_scrofa/Ensembl/Sscrofa9": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna", "variation"],
"Sus_scrofa/NCBI/Sscrofa10": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Sus_scrofa/NCBI/Sscrofa10.2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Sus_scrofa/NCBI/Sscrofa9.2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Sus_scrofa/UCSC/susScr2": ["bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Sus_scrofa/UCSC/susScr3": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Zea_mays/Ensembl/AGPv2": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"],
"Zea_mays/Ensembl/AGPv3": ["gtf", "bed12", "bismark", "bowtie", "bowtie2", "bwa", "star", "fasta", "chromosomes", "abundantseq", "smrna"]
};
var type_nicenames = {
gtf: "GTF",
bed12: "BED",
bismark: "Bismark",
bowtie: "Bowtie 1",
bowtie2: "Bowtie 2",
bwa: "BWA",
star: "STAR",
fasta: "FASTA",
chromosomes: "FASTA (Chromosomes)",
abundantseq: "Abundant Sequences",
smrna: "smRNA",
variation: "Variation",
gatk: "GATK"
};
var type_suffixes = {
gtf: "Annotation/Genes/", // appended to command: genes.gtf
bed12: "Annotation/Genes/", // appended to command: genes.bed
bismark: "Sequence/BismarkIndex/",
bowtie: "Sequence/BowtieIndex/",
bowtie2: "Sequence/Bowtie2Index/",
bwa: "Sequence/BWAIndex/",
star: "Sequence/STARIndex/",
fasta: "Sequence/WholeGenomeFasta/",
chromosomes: "Sequence/Chromosomes/",
abundantseq: "Sequence/AbundantSequences/",
smrna: "Annotation/SmallRNA/",
variation: "Annotation/Variation/",
gatk: ""
};
var manifest = [];
$(function(){
// Initiate clipboard.js
new Clipboard('.prewrap > .btn');
// Get the full file list
try {
$.get('ngi-igenomes_file_manifest.txt', function(data){
try {
manifest = data.match(/[^\r\n]+/g);
$('#file_manifest').html('waiting for selection..');
} catch(e){
$('#file_manifest').html('Error - could not load file manifest.').attr('id', 'file_manifest_error');
console.error(e);
}
}).fail(function() {
$('#file_manifest').html('Error - could not load file manifest.').attr('id', 'file_manifest_error');
});
} catch(e){
$('#file_manifest').html('Error - could not load file manifest.').attr('id', 'file_manifest_error');
console.error(e);
}
// Build our variables
var paths = Object.keys(types);
var genomes = [];
var sources = {};
var builds = {};
for(i=0; i<paths.length; i++){
var s = paths[i].split('/');
if(genomes.indexOf(s[0]) < 0){
genomes.push(s[0]);
}
if(sources[s[0]] == undefined){
sources[s[0]] = [];
}
if(sources[s[0]].indexOf(s[1]) < 0){
sources[s[0]].push(s[1]);
}
if(builds[s[0]+'/'+s[1]] == undefined){
builds[s[0]+'/'+s[1]] = [];
}
builds[s[0]+'/'+s[1]].push(s[2]);
}
// Populate first dropdown
for(i=0; i<genomes.length; i++){
$('#all_genomes').append($('<option>', {
value: genomes[i],
text: genomes[i].replace('_',' ')
}));
}
// LISTENERS!
$('#genome').change(function(e){
e.preventDefault();
// Reset downstream dropdown
$('#build').html('<option value="">Please select a source</option>').attr('disabled', true);
$('#type').html('<option value="">Please select a build</option>').attr('disabled', true);
$('#bucket_url, #sync_command').html('<span class="text-muted">waiting for selection…</span>');
// Set up source dropdown
var g = $(this).val();
if(g == ''){
$('#source').html('<option value="">Please select a genome</option>').attr('disabled', true);
} else {
$('#source').html('').attr('disabled', false);
if(sources[g].length > 1){
$('#source').html('<option value="">[ select ]</option>');
}
for(i=0; i<sources[g].length; i++){
$('#source').append($('<option>', {
value: sources[g][i],
text: sources[g][i]
}));
}
$('#source').trigger('change');
$('#build').trigger('change');
$('#type').trigger('change');
}
});
// Source dropdown
$('#source').change(function(e){
e.preventDefault();
// Reset downstream dropdown
$('#type').html('<option value="">Please select a build</option>').attr('disabled', true);
$('#bucket_url, #sync_command').html('<span class="text-muted">waiting for selection…</span>');
// Set up build dropdown
var g = $('#genome').val();
var s = $(this).val();
var k = g+'/'+s;
if(s == ''){
$('#build').html('<option value="">Please select a source</option>').attr('disabled', true);
} else {
$('#build').html('').attr('disabled', false);
if(builds[k].length > 1){
$('#build').html('<option value="">[ select ]</option>');
}
for(i=0; i<builds[k].length; i++){
$('#build').append($('<option>', {
value: builds[k][i],
text: builds[k][i]
}));
}
$('#build').trigger('change');
$('#type').trigger('change');
}
});
// Build dropdown
$('#build').change(function(e){
e.preventDefault();
// Set up type dropdown
var g = $('#genome').val();
var s = $('#source').val();
var b = $(this).val();
var k = g+'/'+s+'/'+b;
if(b == ''){
$('#type').html('<option value="">Please select a source</option>').attr('disabled', true);
$('#bucket_url, #sync_command').html('<span class="text-muted">waiting for selection…</span>');
} else {
$('#type').html('').attr('disabled', false);
if(types[k].length > 1){
$('#type').html('<option value="">[ select ]</option>');
}
for(i=0; i<types[k].length; i++){
$('#type').append($('<option>', {
value: types[k][i],
text: type_nicenames[types[k][i]]
}));
}
$('#type').trigger('change');
}
});
// Type dropdown
$('#type, #region, #local').change(function(e){ update_cmd(); });
$('#local').keyup(function(e){ update_cmd(); });
function update_cmd(){
var g = $('#genome').val();
var s = $('#source').val();
var b = $('#build').val();
var t = $('#type').val();
var region = $('#region').val();
var local = $('#local').val();
if(g == '' || s == '' || b == '' || t == '' || region == '' || local == ''){
$('#bucket_url, #sync_command, #file_manifest').html('<span class="text-muted">waiting for selection…</span>');
$('#bucket_url_wrapper button, #sync_command_wrapper button')
.removeClass('btn-warning')
.attr('disabled', true);
} else {
// Build path and sync command
var path = g+'/'+s+'/'+b+'/'+type_suffixes[t];
local = local.replace('{genome}',g).replace('{source}',s).replace('{build}',b).replace('{type_path}',type_suffixes[t]);
var s3path = 's3://ngi-igenomes/igenomes/'+path;
var s3cmd = 'aws s3 --no-sign-request --region '+region+' sync '+s3path+' '+local;
if(t == 'gtf'){
s3path += 'genes.gtf';
s3cmd += ' --exclude "*" --include "genes.gtf"';
}
if(t == 'bed12'){
s3path += 'genes.bed';
s3cmd += ' --exclude "*" --include "genes.bed"';
}
$('#bucket_url').html(s3path);
$('#sync_command').html(s3cmd);
$('#bucket_url_wrapper button, #sync_command_wrapper button')
.addClass('btn-warning')
.attr('disabled', false);
// Get the file manifest
if(manifest.length > 0){
var files = '';
for(i=0; i<manifest.length; i++){
if(manifest[i].substr(0, s3path.length) == s3path){
files += manifest[i] + "\n";
}
}
$('#file_manifest').html(files);
}
}
}
// Code example clicks
$('.local_code').click(function(e){
var ns = $('#local').val() + $(this).text();
$('#local').val(ns);
});
});
</script>
</body>
</html>