Bedsect V3.0

sraghav-lab · Nov 4, 2019 · 980a933 · 980a933
commit 980a933
Show file tree

Hide file tree

Showing 195 changed files with 187,170 additions and 0 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/INSTALL.md b/INSTALL.md
@@ -0,0 +1,64 @@
+# Installation Manual
+
+## Minimum System Requirements
+
+* Core 2 Duo Processor or higher
+* 4 GB DDR2 RAM or more
+* Ubuntu 14.04 or later version
+
+## Tools & Dependencies
+
+* Apache2
+* PHP
+* MySQL
+* R & Shiny Server
+* Bedtools
+
+### PHP Modules
+
+* php-common
+* php-mysql
+
+### Perl Modules
+
++ Statistics::Basic
++ cs::Basic
+
+### R packages
+
+UpSetR
+
+corrplot
+
+dplyr
+
+SuperExactTest
+
+shinythemes
+
+shinyjs
+
+# Installation
+
+Start by installing any HTTP server(Apache2) having support for server-side languages like PHP and configure accordingly. Install Bedtools, PHP,  MySQL and R+ Shiny Server followed mentioned modedules/packages.
+
+Clone (`git clone https://github.com/sraghav-lab/BedSect.git`)or download the [Bedsect Github repositoy](https://github.com/sraghav-lab/BedSect/archive/master.zip
+)
+
+Put all the contents from **application** folder to the Apache2 server root directory .
+
+Create a database for Bedsect and import `bedsect_schema.sql `present in **database_schema** directory to the newly created database.
+
+`mysql -u <username> -p dbname<bedsect_schema.sql `
+
+To import the GTRD database schema use the `gtrd_schema.sql` file.
+
+Update the database name, host, username and password in `config.php` file located in the root directory. The config file also contains default installation path and path to Shiny server, update the paths accordingly.
+
+By default the email sending feature is disabled. To enable email sending first update **SMTP** served details in `mail.php` and remove comment form `jobControl.php` line no 25 and `runJob.php` line no 79.
+
+Copy the contents of **shiny** folder to the Shiny server root directory. Default: `/srv/shiny-server`. 
+
+Change the user and group of the `/var/www/html `folder to `www-data:www-data` and set permission of the `server/files` folder to 755.
+
+Navigate to `localhost` or `server-ip-address `and do a test run using the demo data provided in **test_data** folder.
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
@@ -0,0 +1,6 @@
+![alt text](./logo.png)
+
+Bedsect is a web server tool for overlapping genomic regions from multiple datasets.
+
+Please check the [Insatallation Manual](https://github.com/sraghav-lab/Bedsect/edit/master/README.md) for more details.
+
diff --git a/application/.DS_Store b/application/.DS_Store
diff --git a/application/Bedsect_demo.zip b/application/Bedsect_demo.zip
diff --git a/application/about.php b/application/about.php
@@ -0,0 +1,90 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta http-equiv=“Cache-Control” content=“no-cache, no-store, must-revalidate” />
+    <meta http-equiv=“Pragma” content=“no-cache” />
+    <meta http-equiv=“Expires” content=“0" />
+    <meta charset="utf-8">
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+    <meta name="description" content="A far better approach for intersecting bed files">
+    <meta name="author" content=" Some ILS students">
+    <link rel="icon" href="./assets/favicon.ico">
+    <title>About Us</title>
+    <!-- All style files-->
+    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.2/css/bootstrap.min.css">
+    <link href="./assets/css/ie10-viewport-bug-workaround.css" rel="stylesheet">
+ <!--include the nav bash here -->
+	<?php include_once("views/nav.php");?>
+</head>
+<body>
+
+<div class="container" style="border:0px solid #d6d6d6;">
+      <div class="page-header">
+        <h2>About Us</h2>
+        <p class="lead"></p>
+      </div>
+    <div class="panel panel-warning">
+      <div class="panel-heading"><strong>Principal Investigator</strong></div>
+      <div class="panel-body">
+        <div class="col-xs-6 col-xs-offset-3 col-sm-3 col-sm-offset-0">            
+<br>
+<img class="img-responsive img-circle center-block" src="./assets/dsc_0240.jpg">    
+</div><!-- col-sm-3 -->
+
+            <div class="col-xs-12 col-sm-9">
+                <hr class="visible-xs-block">    
+                <!-- .author-box-intro --><div class="author-inline-block">
+                <h4 class="author-box-title">
+                 <span class="author-name text-primary">Dr. Sunil K. Raghav, Ph.D.</span><small class="author-social-links small"><a href="#" class="author-social-link twitter small" target="_blank"><i class="fa fa-x fa-twitter"></i></a><a href="#" class="author-social-link gplus small" target="_blank"><i class="fa fa-x fa-google-plus"></i></a>      </small><!-- author-social-links -->
+                </h4> 
+                </div>
+		<div class="author-box-content">
+Dr. Raghav completed bachelors in science degree from the University of Delhi in 1997 followed by a Masters degree from CCS University, Meerut. After completing M.Sc. he joined as a research fellow in IGIB, Delhi and was awarded Ph.D. in the field of Biotechnology. Prior to joining as a scientist(Ramalingaswami Fellow) at Institute of Life Sciences, Bhubaneswar he worked as a scientist in Laboratory of Systems Biology & Genetics, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland and as a postdoctoral fellow in Molecular Immunology Group, Turku Centre for Biotechnology (BTK), Finland.
+                </div><!-- author-box-content -->
+            </div><!-- col -->
+      </div>
+    </div>
+    <div class="panel panel-warning">
+      <div class="panel-heading"><strong>PhD Students</strong></div>
+      <div class="panel-body">
+        <div class="col-xs-6 col-xs-offset-3 col-sm-3 col-sm-offset-0">
+<br>
+<img class="img-responsive img-circle center-block" src="./assets/gpm.jpg">               
+</div><!-- col-sm-3 -->
+<br>
+            <div class="col-xs-12 col-sm-9">
+                <hr class="visible-xs-block">
+                <!-- .author-box-intro --><div class="author-inline-block">
+                <h4 class="author-box-title">
+                 <span class="author-name text-primary">Gyan Prakash Mishra, MS(Pharm.)</span><small class="author-social-links small"><a href="#" class="author-social-link twitter small" target="_blank"><i class="fa fa-x fa-twitter"></i></a><a href="#" class="author-social-link gplus small" target="_blank"><i class="fa fa-x fa-google-plus"></i></a>      </small><!-- author-social-links -->
+                </h4>
+                </div>
+                <div class="author-box-content">
+Gyan Prakash has done Master degree in Pharmaceutical Sciences from National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata in year 2015. He has qualified GPAT 2013 and DBT-BINC in 2017 (Bioninformatics National Certificate Examination). Gyan is interested to study transcriptional regulation in Dendritic cells upon various Toll-like receptor (TLR) stimulation using Next Generation Sequencing data. He loves to play Badminton and chess.
+                </div><!-- author-box-content -->
+            </div><!-- col -->
+	</div>
+      <div class="panel-body">
+        <div class="col-xs-6 col-xs-offset-3 col-sm-3 col-sm-offset-0">
+<br>
+<img class="img-responsive img-circle center-block" src="./assets/arup.jpg">     
+</div><!-- col-sm-3 -->
+<br><br>
+            <div class="col-xs-12 col-sm-9">
+                <hr class="visible-xs-block">
+                <!-- .author-box-intro --><div class="author-inline-block">
+                <h4 class="author-box-title">
+                 <span class="author-name text-primary">Arup Ghosh, MS(Pharm.)</span><small class="author-social-links small"><a href="#" class="author-social-link twitter small" target="_blank"><i class="fa fa-x fa-twitter"></i></a><a href="#" class="author-social-link gplus small" target="_blank"><i class="fa fa-x fa-google-plus"></i></a>      </small><!-- author-social-links -->
+                </h4>
+                </div>
+                <div class="author-box-content">
+Arup has done Bachelor's in Pharmacy from West Bengal University of Health Science & M.S.(Pharm) from National Institute of Pharmaceutical Education & Research (NIPER-Kolkata). Currenty he is working as a Ph.D. student in Dr. Sunil K Raghav's lab., Institute of Life Sceinces, Bhubaneswar. He enjoys photography, solving math puzzles, blogging rest of the time. 
+                </div><!-- author-box-content -->
+            </div><!-- col -->
+
+        </div>
+    </div>
+  </div><!--container-->
+</body>
+<?php include("views/footer.php");?>
+</html>
diff --git a/application/assets/.DS_Store b/application/assets/.DS_Store
diff --git a/application/assets/.Rhistory b/application/assets/.Rhistory
diff --git a/application/assets/arup.jpg b/application/assets/arup.jpg
diff --git a/application/assets/css/bootstrap-select.min.css b/application/assets/css/bootstrap-select.min.css
diff --git a/application/assets/css/bootstrap.min.css b/application/assets/css/bootstrap.min.css
diff --git a/application/assets/css/home.css b/application/assets/css/home.css
@@ -0,0 +1,24 @@
+/*Css for the homepage*/
+.panel-default>.panel-heading {
+    color: #020101;
+    background-color: #f7c2c2;
+    border-color: #666666;
+}
+.panel{
+    border-color: #666666;
+}
+.alert-danger {
+    color: #b50400;
+    background-color: #f2dede;
+    border-color: #ebccd1;
+}
+.well {
+    min-height: 20px;
+    padding: 19px;
+    margin-bottom: 20px;
+    background-color: #e2edf9;
+    border: 1px solid #666666;
+    border-radius: 4px;
+    -webkit-box-shadow: inset 0 1px 1px rgba(0,0,0,.05);
+    box-shadow: inset 0 1px 1px rgba(0,0,0,.05);
+}
diff --git a/application/assets/css/ie10-viewport-bug-workaround.css b/application/assets/css/ie10-viewport-bug-workaround.css
@@ -0,0 +1,13 @@
+/*!
+ * IE10 viewport hack for Surface/desktop Windows 8 bug
+ * Copyright 2014-2015 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+
+/*
+ * See the Getting Started docs for more information:
+ * http://getbootstrap.com/getting-started/#support-ie10-width
+ */
+@-ms-viewport     { width: device-width; }
+@-o-viewport      { width: device-width; }
+@viewport         { width: device-width; }
diff --git a/application/assets/css/jquery.fileupload.min.css b/application/assets/css/jquery.fileupload.min.css
diff --git a/application/assets/css/jquery.fileupload.min.css.map b/application/assets/css/jquery.fileupload.min.css.map
diff --git a/application/assets/dsc_0240.jpg b/application/assets/dsc_0240.jpg
diff --git a/application/assets/fig_1_bedsect.jpg b/application/assets/fig_1_bedsect.jpg
diff --git a/application/assets/fig_1_bedsect.png b/application/assets/fig_1_bedsect.png
diff --git a/application/assets/fig_2_bedsect.jpg b/application/assets/fig_2_bedsect.jpg
diff --git a/application/assets/fig_2_bedsect.png b/application/assets/fig_2_bedsect.png
diff --git a/application/assets/fig__bedsect.jpg b/application/assets/fig__bedsect.jpg
diff --git a/application/assets/gpm.jpg b/application/assets/gpm.jpg
diff --git a/application/assets/js/app.js b/application/assets/js/app.js
@@ -0,0 +1,98 @@
+// Handles the Bedsect application initiation
+function runApp(){
+    $('#loading').modal('show');
+    event.preventDefault();
+    var gtrd;
+    $('#get_exp tr').each(function(row, tr){gtrd = gtrd + $(tr).find('td:eq(0)').text()+','});
+    gtrd = gtrd.replace('undefined,','');
+    var user = $("#runAPP").val();
+    var email = $("#email").val();
+    var genome = $("#genome").val();
+    var overlap = $("#overlap").val();
+    $.ajax({
+        type: "POST",
+        url: "runJob.php",
+        //url : "testApp.php",
+        data: "user="+user+"&email="+email+"&genome="+genome+"&overlap="+overlap+"&gtrd="+gtrd,
+        success: function(msg){
+            $("#alert").html(msg);
+            $('.modal').modal('show');
+            $('#loading').modal('hide');
+        }
+    });
+};
+
+//Enable or disable the GTRD panel
+function gtrdLoad() {
+    var gtrdSel = document.getElementById('gtrd-check');
+    var gtrdBox = document.getElementById('gtrd-box');
+    if (gtrdSel.checked == true){
+        gtrdBox.style.display = "block";
+    } else {
+        gtrdBox.style.display = "none";
+    }
+};
+
+// Enable tooltips
+$(document).ready(function(){
+  $('[data-toggle="tooltip"]').tooltip();   
+});
+
+//Handle the transcription factor search function
+$(document).ready(function(){
+    //alert('this is great');
+    $('#orgSel').on('change',function(){
+        var organism = $('#orgSel').val();
+        $.ajax({
+            url:'gtrd_search.php',
+            data:{organism:organism},
+            type: 'POST',
+            success:function(data){
+                if(!data.error){
+                    $('#tf_select').html(data);
+                    $('#tf_select').selectpicker('refresh');
+                }
+            }
+        });
+    });
+    $('#tf_select').on('change',function(){
+        var organism = $('#orgSel').val();
+        var tf_select = $('#tf_select').val();
+        $.ajax({
+            url:'gtrd_search.php',
+            data:{organism:organism,search:tf_select},
+            type: 'POST',
+            success:function(data){
+                if(!data.error){
+                    $('#cell_select').html(data);
+                    $('#cell_select').selectpicker('refresh');
+                }
+            }
+        });
+    });
+    $('#cell_select').on('change',function(){
+        var organism = $('#orgSel').val();
+        var tf_select = $('#tf_select').val();
+        var cell_select = $('#cell_select').val();
+        $.ajax({
+            url:'gtrd_search.php',
+            data:{organism:organism,search:tf_select,cell:cell_select},
+            type: 'POST',
+            success:function(data){
+                if(!data.error){
+                    $('#gtrd_result').html(data);
+                }
+            }
+        });
+    });
+    $('#gtrd_result').on('click','.btn-add',function(){
+        var gtrdCheckout = document.getElementById('gtrd_added');
+        var exp = $(this).parents("tr");
+        exp.find('button').replaceWith('<button class="btn btn-danger btn-remove">Remove</button>');
+        $('#gtrd_list').append(exp);
+        gtrdCheckout.style.display = "block";
+    });
+    $('#gtrd_list').on('click','.btn-remove',function(){
+        $(this).parents("tr").remove();
+    });
+});