usearch install on Mac OSX

[Dennis Jakupovic]

Hi all, 

I've got a problem with installing usearch on QIIME 1.8, where I'm just clueless on how to install it (even though there are enough forums discussing it). 

I've downloaded the binary file from drive5.com, but how to move forward from here? Could you guys help me out on this one?

Cheers and many thanks in advance!

Dennis

[Jenya Kopylov]

Hi Dennis,

usearch v5.2.236 is referred to as 'usearch' in QIIME and usearch v6.1 as 'usearch61'.

The best approach is to set a symbolic link to each binary as explained here (usearch Install Notes).

Make sure that the symbolic link is in your $PATH (in the example of the Install Notes, $HOME/bin

should be in the $PATH env variable).

Jenya

[Dennis Jakupovic]

Hi Jenya, 

Thanks for your reply! Sadly, I still haven't managed to make usearch work...

I've downloaded the usearch v5.2.236 file and renamed in two ways.

• via the GUI, just changing the name into usearch, which resulted in just a document file
• via the Terminal (Mac OSX) into usearch, which resulted into a Unix Executable File.

Now my guess is the Unix Executable File should do the trick, right? But when I put it in my path,
e.g ~/bin or in the same directory as my sequences, it just gives the same errors as before
(not installed, wrong version, etc.).

At this point, print_qiime_config.py won't reveal usearch as installed, and
usearch --version remains an unknown command. 

Herefrom I conclude that the 'installation' of usearch has failed, but what went wrong?

Hope this is more informative..

Ciao, 
Dennis

[Jenya Kopylov]

Hi Dennis,

Here are step-by-step instructions of how I installed usearch on my mac,

1. download usearch binary (for Mac OSX) from here (the binary usearch5.2.236_i86osx32 is now in my Downloads folder, I will work from there)

2. check I don't have usearch already installed

$ which usearch 

3. add executable permissions to the usearch5.2.236_i86osx32 binary

$ chmod 755 ./usearch5.2.236_i86osx32 

4. check it's working

$  ./usearch5.2.236_i86osx32 --version

usearch v5.2.236

5. create the symbolic link (I will keep the binary in my Downloads folder as an example)

$ pwd
/Users/jenya/Downloads

$ ln -s /Users/jenya/Downloads/usearch5.2.236_i86osx32 /Users/jenya/Downloads/usearch

6. The "/Users/jenya/Downloads" is not in my $PATH, so I add it (temporarily):

$ export PATH=$PATH:/Users/jenya/Downloads

7. test the symbolic link is working

$ which usearch
/Users/jenya/Downloads/usearch

$ usearch --version
usearch v5.2.236


You would want to move usearch5.2.236_i86osx32 to another directory (not Downloads), somewhere where you

store all your binaries. That directory should probably be in your $PATH already. If not, add it to ~/.bashrc (or

~/.bash_profile) (if you're using the bash script, check using $SHELL) by copying the same "export" command

in (6) above. Adding the directory using "export" from the shell as I did is only temporary to that shell instance.

Hope this helps,

Jenya






/Users/jenya/Downloads/usearch

[Dennis Jakupovic]

Hi Jenya, 

Sorry for the long wait, but I had problems with my data which prevented me from doing the actual analysis. 

The step-by-step instructions you provided worked perfectly, many, many thanks for that.

I've installed usearch in QIIME and did a successful OTU pick with usearch as method on my dataset now. 

Again, superthanks! :)

Dennis