installing usearch on Mac

I am a beginner in the field, trying to install usearch on MAC, I followed the instruction as on the website, but I am not sure if it is correctly installed

I downloaded the file to >> documents/ tutorial Then I used the chmod +x to make it executable

output Nourhans-MacBook-Pro:tutorial nourhanelsahly$ ls -l total 2848 -rwxr-xr-x@ 1 nourhanelsahly staff 1458039 Dec 14 11:36 usearch10.0-2.240_i86osx32

I might be stuck in determining the path, when I use “echo $PATH” I get the following

output Nourhans-MacBook-Pro:tutorial nourhanelsahly$ echo $PATH /anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin

I used the following command

/usr/bin/usearch10.0-2.240_i86osx32 -id 0.9 -cluster_fast reads.fasta -uc results.uc

output Nourhans-MacBook-Pro:tutorial nourhanelsahly$ /usr/bin/usearch10.0-2.240_i86osx32 -id 0.9 -cluster_fast reads.fasta -uc results.uc -bash: /usr/bin/usearch10.0-2.240_i86osx32: No such file or directory

16s sequencing usearch sequencing

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written 8.7 years ago by n.elsahly •

What leads you to believe that? Without access to your Mac we can't really help you unless you can tell us why and in what way it does not work.

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written 8.7 years ago by GenoMax

@genomax is quite correct here. Edit your post with the exact errors you get while installing/running it.

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written 8.7 years ago by Shab86

The location /documents/tutorial isn’t in your PATH, so the file isn’t found.

You need to either execute the code directly ./usearch10.0-2.240_i86osx32 (While you are inside the tutorial folder) or ensure that the folder is added to the PATH:

export PATH=$PATH:/Documents/tutorial

Or move the usearch file in to one of the locations already in the path, though that’s not always a good idea.

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written 8.6 years ago by Joe

1 answer

You can't "install" usearch, just download the application for Mac and execute it through command line (e.g. ./usearch -command1 -input -output).

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written 8.7 years ago by sten1987 •

Yes, that was what I did.

I downloaded the file to >> documents/ tutorial Then I used the chmod +x to make it executable

output

Nourhans-MacBook-Pro:tutorial nourhanelsahly$ ls -l
total 2848
-rwxr-xr-x@ 1 nourhanelsahly  staff  1458039 Dec 14 11:36 usearch10.0-2.240_i86osx32

I am stuck in determining the path

when I use “echo $PATH” I get the following

Nourhans-MacBook-Pro:tutorial nourhanelsahly$ echo $PATH
/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin

then I used the following command

/usr/bin/usearch10.0-2.240_i86osx32 -id 0.9 -cluster_fast reads.fasta -uc results.uc

output

Nourhans-MacBook-Pro:tutorial nourhanelsahly$ /usr/bin/usearch10.0-2.240_i86osx32 -id 0.9 -cluster_fast reads.fasta -uc results.uc
-bash: /usr/bin/usearch10.0-2.240_i86osx32: No such file or directory

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updated 8.6 years ago by GenoMax

• written 8.6 years ago by n.elsahly •

First find out the full path to the directory you are in when you first did the ls -l command by using pwd.

Take the output of pwd command and then use it to append to your $PATH by doing export PATH=$PATH:output_of_pwd (replace the real value for output_of_pwd). At this point you should be able to run usearch (you can't use /usr/bin/... unless your usearch executable is in that directory.

If you intend to do this properly then spend a couple of hours here learning basics of UNIX and file system.

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written 8.6 years ago by GenoMax

Thank you so much, it was really helpful

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written 8.6 years ago by n.elsahly •