Question: installing usearch on Mac
0
gravatar for n.elsahly
2.2 years ago by
n.elsahly0
n.elsahly0 wrote:

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

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by n.elsahly0

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.

ADD REPLYlink written 2.2 years ago by genomax78k

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

ADD REPLYlink written 2.2 years ago by Shab86240

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.

ADD REPLYlink written 2.2 years ago by Joe16k
0
gravatar for sten1987
2.2 years ago by
sten19870
sten19870 wrote:

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

ADD COMMENTlink written 2.2 years ago by sten19870

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
ADD REPLYlink modified 2.2 years ago by genomax78k • written 2.2 years ago by n.elsahly0

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.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by genomax78k

Thank you so much, it was really helpful

ADD REPLYlink written 2.2 years ago by n.elsahly0
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