See also:
Problems installing and running
USEARCH
Quick start
Command line
Binary
filename
USEARCH is a stand-alone
binary
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 rename the binary file
to usearch to avoid typing long names like usearch6.0.98_i86linux32.
Missing DLL problem in Windows
See here if you get missing a vcomp100.dll error.
Execute permissions
Under Linux and OSX you must ensure that you have read and execute
permissions for the binary file. If needed, use the chmod command to set the
execute bit, e.g.:
chmod +x
/usr/bin/usearch6.0.98_i86linux32
PATH or pathname
The binary
file must be in one of the directories specified in your PATH variable,
or you must type the full path to the file, e.g. for
Linux:
/usr/bin/usearch6.0.98_i86linux32 -id 0.9
-cluster_fast reads.fasta -uc results.uc
Under the Windows CMD shell, path names
are separated by backslashes, e.g.:
C:\MyPrograms\usearch6.2.98_win32.exe -id 0.9
-cluster_fast reads.fasta -uc
results.uc
Run USEARCH
from a shell
USEARCH will not
work if you try to start it in a graphical interface like
Windows Explorer or the Mac Finder. You must start it from a
command window or shell.
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Platform |
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How to get a command-line interface |
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Linux |
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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'. If you don't know
how to get a shell prompt, 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. |
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Mac OSX |
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Look for the Terminal command
under Applications > Utilities. This will give you a shell
prompt similar to Unix and Linux. If you're not familiar with using
shell commands, you're probably going to have trouble figuring out
how to use my programs; I recommend getting a colleague to help you
who is familiar with using command-line
programs. |
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Windows |
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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. |
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Windows with Cygwin |
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If you're familiar with using
Unix or Linux shells, you might want to check out the Cygwin 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. |
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