-
Notifications
You must be signed in to change notification settings - Fork 0
/
index.html
173 lines (160 loc) · 7.19 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>Bioinformatics software list available on DATARMOR</title>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
<script type="text/javascript" src="./js/jquery-1.11.1.min.js"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha384-aJ21OjlMXNL5UyIl/XNwTMqvzeRMZH2w8c5cRVpzpU8Y5bApTppSuUkhZXN0VxHd" crossorigin="anonymous"></script>
<script type="text/javascript" src="./js/d3.4.2.6.min.js" charset="utf-8"></script>
<script type="text/javascript" src="./js/keshif.js" charset="utf-8"></script>
<script type="text/javascript" src="./helpin/helpin_material.js" charset="utf-8"></script>
<script type="text/javascript" src="./helpin/helpin.js" charset="utf-8"></script>
<script type="text/javascript" src="./js/papaparse.min.js" charset="utf-8"></script>
<link rel="stylesheet" href="./css/keshif.css"/ type="text/css">
<link rel="stylesheet" href="./font-awesome/css/font-awesome.min.css">
<link rel="stylesheet" href="./helpin/helpin.css" type="text/css">
<link rel="stylesheet" href="./css/software_browser.css" type="text/css">
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha384-HSMxcRTRxnN+Bdg0JdbxYKrThecOKuH5zCYotlSAcp1+c8xmyTe9GYg1l9a69psu" crossorigin="anonymous">
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/3.4.1/css/bootstrap-theme.min.css" integrity="sha384-6pzBo3FDv/PJ8r2KRkGHifhEocL+1X2rVCTTkUfGk7/0pbek5mMa1upzvWbrUbOZ" crossorigin="anonymous">
<script type="text/javascript">
//
var socialShare = false, demoHeader = false;
//
function formatToolName(toolName){
var idx=toolName.lastIndexOf("-");
var str="<span class='toolName'>";
if (idx<0){
return str+toolName+"</span> ";
}
str+=toolName.substring(0,idx).trim();
str+="</span> - <span class='toolVersion'>";
str+=toolName.substring(idx+1).trim();
str+="</span> ";
return str;
}
function formatCmdLine(appPath, toolName){
var str="Cmd-line </span><span class='topicsstd'>(";
str+=appPath;
str+=")</span>";
return str;
}
function formatVersions(versionClass, versionName){
var str="<div><span class='topics topicsbold'>";
str+=versionClass;
str+=":</span><span class='topics'>";
str+="<br>";
str+="<ul>";
var a = versionName.split(","), i;
for (i = 0; i < a.length; i++) {
str+="<li>";
var b = a[i].split("-");
if (b[1] == 'conda'){
str+=b[0]+" - <img src=https://upload.wikimedia.org/wikipedia/commons/e/ea/Conda_logo.svg height=12 >"
} else if (b[1] == 'docker'){
str+=b[0]+" - <img src=https://upload.wikimedia.org/wikipedia/commons/7/79/Docker_%28container_engine%29_logo.png height=12 >"
} else if (b[1] == 'singularity'){
str+=b[0]+" - <img src=https://sylabs.io/wp-content/uploads/2022/03/singularity-logo-round.svg height=12 >"
} else if (b[1] == 'Nextflow'){
str+=b[0]+" - <img src=https://upload.wikimedia.org/wikipedia/commons/6/60/Nextflow_logo.png height=12 >"
} else if (b[1] == 'Snakemake'){
str+=b[0]+" - <img src=https://upload.wikimedia.org/wikipedia/commons/c/c7/Snakemake_logo_dark.png height=12 >"
} else {
str+=b[0]+" - <img src=https://upload.wikimedia.org/wikipedia/commons/8/82/Gnu-bash-logo.svg height=12 >"
}
str+="</li>";
}
str+="</ul>";
str+="</span></div>";
return str;
}
function formatSimpleTopics(topicClass, topicName){
var str="<div><span class='topics topicsbold'>";
str+=topicClass;
str+=": </span><span class='topics'>";
str+=topicName;
str+="</span></div>";
return str;
}
google.charts.setOnLoadCallback(function(){
browser = new kshf.Browser({
domID: "#Software_Browser",
barChartWidth: 160,
leftPanelLabelWidth: 150,
recordName: "softwares",
rightPanelLabelWidth: 90,
source: {
//Three possible solutions to load a data file:
// solution 1: using Google Docs, e.g.:
//gdocId: '1Kf3WkhhhnUn9hclYh2erI6tSpiLgLum5mYtOO_3rxnQ',
// solution 2: using a URL, e.g.:
//dirPath: "http://localhost/~ifremer/ToolDirectory/test/",
// solution 3: using a relative path (to this script), e.g.:
dirPath: "./",
fileType: 'csv',
// note that using 'dirPath' and 'fileType' are only relevant
// for solutions 2 and 3; see Keshif doc for more details
// (https://github.com/adilyalcin/Keshif/wiki/Docs:-Loading-Data).
//Name of data table containing list of softwares
tables: "Softwares"
},
summaries: [
{ name: "Topic", catSplit : ","},
{ name: "Operation", catSplit : ","},
{ name: "Environment", catSplit : ","},
{ name: "Galaxy"},
{ name: "Workflow"},
],
recordDisplay: {
sortColWidth: 45,
sortBy: { title: 'id', inverse: true },
textSearch: "Name",
detailsToggle: "one",
recordView: function() {
// console.log(Object.values(this));
var appliPathPrefix = "DATARMOR:";
var str="";
str+="<div class=''>";
str+=formatToolName(this.Name);
str+="<a class='pubLink fa fa-external-link externallink' target='_blank' href='";
str+=this.Doc;
str+="'> Documentation</a>";
str+="</div>";
str+="<span class='item_details'>";
str+="<div class='topicsbold'>";
str+=this.Description;
str+="</div>";
str+=formatSimpleTopics("Category", this.Operation);
str+=formatSimpleTopics("Topic", this.Topic);
str+=formatVersions("Versions", String(this.Version));
return str;
}
}
});
});
</script>
</head>
<body>
<div class="alert alert-info" >
<h3>Bioinformatics softwares</h3>
<p class="lead">Find here softwares available on DATARMOR cluster to carried out bioinformatics data processing.</p>
</div>
<div class="contents" style="margin-left: 10px;">
<div id="Software_Browser"></div>
<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">Help</h3>
</div>
<div class="panel-body">
<h3 class="mt-5">You do not find a software of interest?</h3>
<p class="lead"><a href="https://w3z.ifremer.fr/bioinfo/Cmdline-Datarmor/Ressources-disponibles/Demande-d-ajout-d-un-nouvel-outil">Click here</a> to request a new software installation.</p>
</div>
</div>
<div id="Infobox"> Data compiled from DATARMOR |
Topic and Operation rely on <a href="http://ifb-elixirfr.github.io/edam-browser" target="_blank">EDAM ontology</a> |
<span class="fa fa-github"></span> Made with
<a href="https://github.com/ifremer-bioinformatics/ToolDirectory" target="_blank">ToolDirectory</a> </div>
</div>
</body>
</html>