-
Notifications
You must be signed in to change notification settings - Fork 1
/
install.html
126 lines (114 loc) · 9.31 KB
/
install.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
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html lang="en">
<head>
<meta http-equiv="Content-Language" content="en-us">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<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">
<title>Installing USEARCH</title>
<link rel="stylesheet" type="text/css" href="stylesx.css">
<style type="text/css">
body.c7 {background-color:#c0c0c0;}
div.c6 {position:absolute; top:45px; left:20px; width:830px; background-color:#ffffff; border-width:10px; border-style:solid;border-color:white;}
td.c5 {background-color: #FFFFCC}
td.c4 {background-color: #E1E1E1}
span.c3 {font-weight: bold}
span.c2 {background-color: #FFFF00}
div.c1 {position:absolute; top:10px; left:20px; width:850px; height:60px;}
.TopButtonPara { color:white; background-color:rgb(50,100,150); border-color:rgb(50,100,150); font-family:Arial, Helvetica, sans-serif; font-weight:normal; font-size:9pt; text-align:center; border-width:4px; border-style:solid; }
.TopButton { color:white; }
a.TopButton:link { text-decoration:none; }
a.TopButton:visited { text-decoration:none; }
a.TopButton:hover { color:orange; }
.NewButtonPara { color:white; background-color:rgb(50,100,150); border-color:rgb(50,100,150); font-family:Arial, Helvetica, sans-serif; font-weight:normal; font-size:9pt; text-align:center; border-width:4px; border-style:solid; }
.NewButton { color:white; }
a.NewButton:link { text-decoration:none; }
a.NewButton:visited { text-decoration:none; }
a.NewButton:hover { color:orange; }
.SideButtonPara { color:white; font-family:Arial, Helvetica, sans-serif; font-size:9pt; font-weight:normal; text-align:center; line-height:18px; }
.SideButton { color:white; }
a.SideButton:link { text-decoration:none; }
a.SideButton:visited { text-decoration:none; }
a.SideButton:hover { color:orange; }
</style>
</head>
<body style="background-color:#c0c0c0;">
<div><a href="https://drive5.com/usearch">
<img alt="USEARCH v12" style="position:absolute; top:40px; left:10px; padding:0px; border:0px;" src="usearch12_banner.jpg"></a></div>
<div style="position:absolute; top:115px; left:10px; width:850px; background-color:#ffffff; min-height:500px">
<div style="position:relative; float:left; background-color:#696969; width:125px; left: 0px; min-height:500px; padding:5px; height: 125px;">
<div class="SideButtonPara" style="text-align:center; padding-top:5px;">
<a class="SideButton" href="index.html">
Docs home
</a>
<br />
<hr style="border:0; border-bottom: 1px solid white;" />
<a class="SideButton" href="cmds.html">
Commands
</a>
<br />
<a class="SideButton" href="topics.html">
Topics
</a>
<br />
<a class="SideButton" href="citation.html">
Publications
</a>
<br />
</div>
</div>
<div class="ManText" style="left:20px; position: absolute; left:135px; width:695px; background-color:white; padding:10px">
<h1>Installing USEARCH</h1>
<p class="ManText"><span class="ManText"> <br>
<b>See also:<br></b> <a href="problems_running.html">Problems installing and running USEARCH</a><br>
<a href="bitness.html">32-bit and 64-bit binaries</a><br>
<a href="cmdline.html">Command line</a><br>
<a href="binary_filename.html">Binary filename</a></span><br>
<a href="multiple_versions.html">Installing multiple versions on the same computer</a></p>
<p class="ManText"><span class="ManText c3">There is no installer -- <span class="c2">don't double-click on the download filename</span></span><b><span class="c2">!</span><br></b>USEARCH is distributed as one file, known as the binary file or executable file. It is completely self-contained: it does not require configuration files, environment variables, third-party libraries or other external dependencies. There is no setup script or installer because they're not needed. To install it, all you do is download or copy the binary to a directory that is accessible from the computer where you want to run the code. For convenience, you may want to <a href="binary_filename.html">rename the binary file to usearch</a> to avoid typing long names like <span class="ManText">usearch6.0.98_i86linux32.</span></p>
<p class="ManText"><span class="ManText"><b>No graphical user interface<br></b> USEARCH does not have a GUI.</span> USEARCH <span class="c2">will not work</span> if you try to start it <span class="c2">in a graphical interface</span> like Windows Explorer or the Mac Finder. You <span class="c2">must run USEARCH from within a command window or shell</span>. <span class="ManText">See table below for how to get a shell prompt. If you're not familiar with using command-line programs, you're probably going to have trouble figuring out how to use USEARCH -- I recommend getting a colleague to help you who is familiar with using command-line programs.</span></p>
<p class="ManText"><span class="ManText"><b>Execute permissions<br></b> Under Linux and OSX you must ensure that you have read and execute permissions for the binary file. If needed, use the <a href="http://en.wikipedia.org/wiki/Chmod">chmod command</a> to set the execute bit, e.g.:</span></p>
<p class="ManText"><span class="ManText">chmod +x /usr/bin/usearch6.0.98_i86linux32</span></p>
<p class="ManText"><span class="ManText"><b>PATH or pathname<br></b> The binary file must be in one of the directories specified in your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH</a> variable, or you must type the full path to the file, e.g. for Linux:</span></p>
<p class="ManText"><span class="ManCode">/usr/bin/usearch6.0.98_i86linux32 -cluster_fast reads.fasta -id 0.9 -uc results.uc</span></p>
<p class="ManText"><span class="ManText">Under the Windows CMD shell, path names are separated by backslashes, e.g.:</span></p>
<p class="ManText"><span class="ManCode">C:\MyPrograms\usearch6.2.98_win32.exe -id 0.9 -cluster_fast reads.fasta -uc results.uc<br>
<br></span> <b>How to get a shell prompt</b></p>
<div align="center">
<table summary="Table" border="0" width="80%" cellspacing="0" cellpadding="5">
<tr>
<td class="c4" width="94" align="right" valign="top"><span class="ManText c3">Platform</span></td>
<td class="c4" align="center" width="8" valign="top"> </td>
<td class="c4" align="left" valign="top"><span class="ManText c3">How to get a command-line interface</span></td>
</tr>
<tr>
<td class="c5" width="94" align="right" valign="top"><span class="ManText">Linux</span></td>
<td class="c5" valign="top" align="center" width="8"> </td>
<td class="c5" valign="top" align="left"><span class="ManText">There are many different graphical interfaces and configurations for Linux and Unix, too many that I can cover them all. Look for an icon labeled something like ''Shell', 'Command window' or 'Terminal'.<br>
</span></td>
</tr>
<tr>
<td class="c4" width="94" align="right" valign="top"><span class="ManText">Mac OSX</span></td>
<td class="c4" valign="top" align="center" width="8"> </td>
<td class="c4" valign="top" align="left"><span class="ManText">Look for the Terminal command under Applications > Utilities. This will give you a shell prompt similar to Unix and Linux.<br>
</span></td>
</tr>
<tr>
<td class="c5" width="94" align="right" valign="top"><span class="ManText">Windows</span></td>
<td class="c5" valign="top" align="center" width="8"> </td>
<td class="c5" valign="top" align="left"><span class="ManText">You can get a command-prompt by navigating Start > All Programs > Accessories > Command Prompt, or similar, depending on which version of Windows you're using. You can also use Start > Run, and type CMD or CMD.EXE when prompted for the name of the program to run.<br>
</span></td>
</tr>
<tr>
<td class="c4" width="94" align="right" valign="top"><span class="ManText">Windows with Cygwin</span></td>
<td class="c4" valign="top" align="center" width="8"> </td>
<td class="c4" valign="top" align="left"><span class="ManText">If you're familiar with using Unix or Linux shells, you might want to check out the <a href="http://cygwin.org">Cygwin</a> environment: it's a really good Linux emulator for Windows that includes shells (sh, bash, csh, tsh etc.) and a huge number of standard Linux utilities (ls, grep, tar, ssh and so on). The *win32.exe or *win64.exe binaries run fine under Cygwin, though there can be subtle issues with file names and path names because the native build doesn't understand Cygwin-specific stuff like mount points. As a general rule, you can use Windows paths under Cygwin, including drive letters. You can use forward- or back-slashes in the path name, though you have to be careful with back-slashes because they're significant for the shell; usually it's easier to use forward slashes.</span></td>
</tr>
</table>
</div>
</div>
</div>
</body>
</html>