mirror of
https://github.com/Novartis/cellxgene-gateway.git
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72 lines
2.8 KiB
HTML
72 lines
2.8 KiB
HTML
<!--
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Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
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under the Apache License, Version 2.0 (the "License"); you may not use
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this file except in compliance with the License. You may obtain a copy
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of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
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required by applicable law or agreed to in writing, software distributed
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under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
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OR CONDITIONS OF ANY KIND, either express or implied. See the License for
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the specific language governing permissions and limitations under the License.
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-->
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<html>
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<head>
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<title>Cellxgene Gateway</title>
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<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
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<link rel="stylesheet" href="{{ url_for('static', filename='css/homepagestyle.css') }}">
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<link rel="icon" type="image/png" href="{{ url_for('static', filename='nibr.ico') }}">
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{% for script in extra_scripts %}
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<script src="{{ script }}"></script>
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{% endfor %}
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<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
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<style>
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li {
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font-size: 20px;
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}
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</style>
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</head>
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<body>
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<header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
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<h3>Cellxgene Gateway - HOME</h3>
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</header>
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<br>
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<h1 style="padding-left:35px">
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Links:
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</h1>
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<div class="list-group" style="width:50%;padding-left:65px">
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<a href="{{ url_for('filecrawl') }}" class="list-group-item list-group-item-action">
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<u>File Crawler: Allows you to view all uploaded data.</u></a>
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</div>
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<div class="list-group" style="width:50%;padding-left:65px">
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<a href="{{ url_for('do_GET_status') }}" class="list-group-item list-group-item-action">
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<u>Cache Status: view status of launched cellxgene servers.</u></a>
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</div>
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<br>
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<h1 style="padding-left:35px">
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How To Upload Data via SSH and SCP:
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</h1>
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<ol style="padding-left:85px;">
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<li>
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Confirm that your ssh key has been properly added. Running the following command should connect you to the server:
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</li>
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<pre>ssh ec2-user@{{ ip }}</pre>
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<li>
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Prepare your data on your own machine. They should be in a common folder called 'USER' and should look <br>similar to the following structure:
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</li>
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<pre>- USER
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- hpc.h5ad
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- pbmc3k.h5ad</pre>
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<li>Copy your data to the server (replace USER with your username):</li>
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<pre>ssh ec2-user@{{ ip }} 'mkdir -p {{ cellxgene_data }}/USER/'
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ssh ec2-user@{{ ip }} 'mkdir -p {{ cellxgene_data }}/USER/DATA/'
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scp -r pbmc3k.h5ad ec2-user@{{ ip }}:{{ cellxgene_data }}/USER/DATA/</pre>
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<li>Take a look at your data using the file crawler link above</li>
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</ol>
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</body>
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</html>
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